Some strange updates going on when I uninstall some

KB3004394 was initially released in December - and caused major problems to a lot of users, so was withdrawn the next day.
KB3024777 was then released to uninstall KB3004394 - it also removed its entry from the Installed Updates listing, and left no trace of itself behind
KB3004394 was re-released as v2 (with no known problems) in February - and should show as such in the Installed Updates listing and the History

I have no record of KB3029944 or KB3001652 being installed on my system.

KB3001652 is an update for Visual Studio 2010 for Office - which may explain why I don't have it - and was issued, withdrawn, and re-issued in February... see here for the full story Botched Windows patch KB 3001652 re-issued and appears to be working | InfoWorld

KB3029944 is a replacement for KB3013126 - which I have in my History but not in the Installed listing.
It's always possible (but maybe unlikely?) that 3029944 is also part of another update, or has itself been updated further.

AirPower4ever said:

OK, did some more poking around and I found a great link at the Microsoft forums about this. In the thread it states the problem of the Disk Cleanup and in the case of two updates. I wonder if disk cleanup goes beyond just those two updates mentioned about halfway down on page 4. Thought I would share though

KB3023607 repeatedly removed by deepclean after - Microsoft Community

The thread you're linking to was started by yours truly under the username "Pink_Freud" (I'm a big Pink Floyd fan as you can see) I wrote about it previously on a couple of threads here & here. This post & the 4 links below describe the problems (there are many) of the FUBAR re-release of the previously FUBARed/rescinded patch KB2949927 from OCT 2014:

Patch Tuesday: October's Rescinded 2949927 Gets Reissued as 3033929
Patch Tuesday: Is KB3033929 Causing Problems?
MS Update 3033929 Causing Reboot Loop
My latest Microsoft update problem

I'll try to address your questions/ concerns/ etc from your OP below with my findings inline & bold text with (#) footnotes listed below. Hold onto your hats, cuz it's gonna be a stormy ride...

AirPower4ever said:

First - in other threads I read people were having the same issue after they used the Disk Clean in Win7. I did the same and I had the same problem. So I installed them and they went away; double checked the entries in the WU history and they were there again (2nd time installed). But my issue did not go away so I went back to uninstall all my updates since February since that's when all this started. I started to have Explorer crashes...

Disk Cleanup - Windows Update Cleanup is falsely detecting some updates (only on some user's comps) as "superseded" and removing them. In my case it removes KB3023607(1) & KB3035131(2)

So I kept three kernel updates installed (KB3033929, KB3035131 and KB3013455) and I also kept my Office 2010 and Internet Explorer 11 updates installed. So this is what happened that I find strange...

KB3013455 is superseded by KB3034344 (March 2015)

a) Looking at my records I never installed KB3004375 on any of my systems....When I rebooted KB3004375 was no longer offered; at least that's what I thought. I looked under WU history and nothing there; matching my spreadsheet. But in the control panel area there it was; installed. So that is a mystery. I did uninstall it though and it is back as being offered.

KB3004375 is (yet another) of Micro$loppy's "bundled" updates. See Advisory FAQ's How do I get this update? here: Microsoft Security Advisory 3004375 (3)

b) There are several updates from that time period that show installed per my spreadsheet and confirmed in WU history area, but they are not listed in the control panel area. They are KB3004394, KB3031433, KB3029944 and KB3001652.

KB3004394 is superseded by KB3033929. I have no record of KB3031433 nor does Microsoft Update Catalog or Google search (only hit is your OP), typo perhaps? KB3029944 is superseded by KB3035132. KB3001652 is for users w/ Office installed (4)

These are not listed in the control panel area so I could not uninstall these updates from the February and March releases. So I tried using a command line uninstall and I get a message stating that these are not installed...I don't know how to uninstall these so they are still on my systems...

Windows Updates History is exactly that; it includes the ENTIRE history, listing not only updates presently installed, but past updates subsequently superseded & failed updates (if any). A more accurate reading of what's presently installed is to search Installed Updates; open Windows Update, lower left hand column click "Installed Updates" search box upper right corner you can search KB's by #, range, etc. I hope this clarifies things a bit, if not just ask.:)

c) When I did the uninstall I also updated my spreadsheet per KB update... I am off by one so I checked and I found that KB3031432 is being offered, but I never uninstalled KB3031432 because it was not in the control panel area to uninstall. So that is another issue.

I suspect (but could be wrong) Windows Update Cleanup is incorrectly removing KB3031432 as superseded on your computer

(1) Fixes TLS Poodle vulnerability, is actually a "child product" of KB's 3021952 & 3032359 Feb & March IE Cumulative Updates respectively.

>>>KB3021952: Are there additional updates I should be aware of?
Yes. There are additional fixes for Internet Explorer 11 that are included as part of update 3021952.
For Internet Explorer 11 on Windows 7 Service Pack 1 and Windows Server 2008 R2 Service Pack 1:

• When you install security update 3021952, update 3023607 will also be installed automatically. Update 3023607 changes Transport Layer Security (TLS) protocol renegotiation and fallback behavior.
• When installation is complete, updates 3021952 and 3023607 will be listed in Installed Updates.
• If you download and install updates manually, when you click Download you will be prompted to select updates 3021952 and 3023607.
• For more information, see Microsoft Knowledge Base Article 3023607.
• XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
• KB3032359: Are there additional updates for Internet Explorer that I should be aware of?
  Yes. There is an additional fix for Internet Explorer 11 that is included as part of update 3032359.
  For Internet Explorer 11 on Windows 7 Service Pack 1 and Windows Server 2008 R2 Service Pack 1:
• If you have not installed security update 3021952 (See Microsoft Security Bulletin MS15-009), when you install update 3032359, update 3023607 will also be installed automatically. Update 3023607 changes Transport Layer Security (TLS) protocol renegotiation and fallback behavior.
• When installation is complete, updates 3032359 and 3023607 will be listed in Installed Updates.
• If you download and install updates manually, when you click Download you will be prompted to select updates 3032359 and 3023607. If you have installed security update 3021952, you do not need to reinstall update 3023607.
• For more information, see Microsoft Knowledge Base Article 3023607. <<<

(2) Kernel Patch also "bundled" with KB3033929. Too FUBAR to even try to make sense of IMHO.
(3) Another bungled bundled update mess. How do I get this update?
The functionality discussed in this advisory can be obtained by installing the 3004375 update directly (see Microsoft Knowledge Base Article 3004375). Note that the update is also bundled with the updates being released in MS15-011 (see Microsoft Knowledge Base Article 3000483) and MS15-015 (see Microsoft Knowledge Base Article 3031432). Either update will install the 3004375 update automatically.
(4) This update installs the Visual Studio 2010 Tools for Office Runtime. This is required to run Microsoft Office-based solutions that are built by using Microsoft Visual Studio 2010, Visual Studio 2012, and Visual Studio 2013.
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Whew, that was quite a workout, I need a shower, drink & cup of coffee... not necessarily in that order

Regards,
"UBM" aka "Pink_Freud"