Start up Repair keeps coming up after windows updates

What media are you using for your basic install?

Please follow the Windows Update Posting Instructions and post the requested data
If the file is too large (8MB compressed), remove the older CBSPersist cab files until the final file is below the limit - you can always post them separately after zipping them. (the forum doesn't allow the upload of bare CAB files, for a number of reasons)

Strange
Please open an Elevated Command Prompt, and run the following commands

DIR C:\Windows\Logs\CBS
DIR C:\Windows\Logs\CBS /AH
ICACLS C:\Windows\Logs\CBS
ICACLS C:\Windows\Logs\CBS\CBS.log
ICACLS C:\Windows\Logs\CBS\CheckSUR.log
DIR C:\Windows\pending.* /S


Post the results.

Here are some instructions to make life easier :)
1) To open an Elevated Command Prompt Window (the ECP window), click on Start, All Programs, Accessories – then right-click on Command Prompt, and select Run as Administrator. Accept the UAC prompt.
2) To run the commands easier, highlight the block of commands, and right-click on the highlight – select Copy. In the CP Window, click on the black/white icon at top left – select Paste. The commands will run but may not complete the last command, so hit the Enter Key once.
3) To copy the results... click on the Black/White icon in the top left, and select Edit... 'Select All', and hit the Enter key - then use Ctrl+V or r-click+Paste to paste it into your response.

The problem seems to be related to the Windows Update Agent - and a locked Hardlink operation.


Please download and save the CheckSUR tool from http://support.microsoft.com/kb/947821
(you'll need to look in the details for Windows 7, downloading from the Microsoft Download Center)

Run it - The tool can take anywhere from 5 mins to a couple of hours to run (or 'Install') depending on how much it has to do, and may exit silently - it may appear to freeze for most of that time, but be patient.
The result is logged in the C:\Windows\Logs\CBS\CheckSUR.log file - and an archive …\checksur.persist.log file

Then zip the CheckSUR.log and upload it to your reply.

Unfortunately, it found nothing to fix

My other WU experts are on holiday for at least this week - or I'd have asked them to have a look in.
Given the long delay in waiting for them, I think your best bet is going to be to attempt a Repair install (if it works, it should fix things, and if not it shouldn't harm things)

See the instructions here - Repair Install

Short-term, no - Long-term, your system is likely to get progressively more unstable, until it gets to the point where you'll have to do a clean install, rather than a repair. It will also become progressively more vulnerable to malware.