I've solved the problem for myself by using system restore to go back to before i used gflags. I notice now that gflags does come with the warning:
Note Incorrect use of this tool can degrade system performance or prevent Windows from starting, requiring you to reinstall Windows.
So i probably should have been more careful.
If anyone has a better way to fix this than system restore, like a list of the registry entries that gflags changes and what they should be by default, that would still be very helpful.