Windows keeps booting in Safe Mode after msconfig change

Hi! I had a malware and decided to run malwarebytes anti-malware in safe mode. The problem was that my computer took too long to boot up before it lets me choose my operating system (i also have linux mint installed, just FYI) and I didn't want to wait 10 minutes just to miss hitting F8 so I changed msconfig to automatically load in Safe mode, so i went ahead and checked that. It booted up fine in safe mode, malarebytes found nothing (I also ran this in normal windows right before...again just FYI).

Now the problem is that I cant get out of safe mode. I tried changing msconfig back but it wouldnt save the settings and the check box that I had checked on normal windows (on the second tab) was unchecked and wouldnt even let me interact with it. I even tried selecting 'normal mode' on the first tab. Anything I did to it would result in a message saying 'windows configuration could not be saved' or something (I'm at work, I don't remember exactly what the message was but I will post it later) after I clicked ok or apply.

I also waited and pressed F8 to select how I wanted to boot and went to normal mode and it still went into safe mode. I tried repairing too but it didn't even find an operating system on my computer, but that probably has to do with the fact that I use linux to boot up.

Any ideas on what to try next?

Thanks in advance

To Remove Linux take look at this post:
Error 0xc0000225 on boot

I think restoring the MBR of Windows OS might help. A good PM should be able to do that.

Otherwise do what theog has suggested although you may not like to remove Linux.

PS: This Forum has a tutorial to restore Windows 7 MBR here:

MBR - Restore Windows 7 Master Boot Record

You may like to go through it.

I did not want to remove linux and removing it would have probably done nothing for me, as it is on a whole separate hard drive (my laptop has two).

I somehow solved it, and not quite sure how. I put in the Windows 7 DVD while in Safe Mode and in an act of desperation tried to see if I could somehow make it work with that. I put it in and fiddled with it and somehow there was a restore point of the day I decided to boot into safe mode. I restored it and restarted, my computer still for some reason booted into Safe Mode. I went into msconfig and this time Safe Mode was checked on the second tab. I unchecked it, and restarted and it started up normally.

Lesson learned: Never automatically boot up into Safe Mode using msconfig unless you absolutely have to.