This article seems to have some information that may help. It does go over some steps you may have already tried (ntregopt), but it includes a link to a tool you may have yet to try to clean your registry of dead entries: vxscrub.
I'm not big on these registry cleaners, but some people rave about ccleaner, which contains a module that also cleans your registry of dead entries.
Personally, I would opt for a data backup and an operating system re-install for a more stable system. That depends on your environment and available time, though.
I found this post which seems to imply that this error is caused by a corrupted swap file. Since you've already tried the first suggestion in the post, I would try the second, added recommendation (cross posted here for easy reference):
The page file needs to be overwritten as it has been corrupted. Follow the following steps:
- Enter System in control panel (classic view)
- Click on the Advanced tab
- Click the settings button under "performance"
- Click the Advanced tab in Performance Settings
- Click Change virtual settings
- Choose No paging file on the settings and click Set
- Exit and restart the computer.
- Repeat the first five steps of these instructions.
- Choose System managed size on the settings and click Set
- When you exit you will be asked if you want to overwrite the previous page file. Allow this action.
- Restart your computer. You will be rid of the error message. Also, your programs may run better.
I still think it could be a corrupted swap file. Have a look at this document, which outlines the procedure a lot more. Are you sure you removed the swap file, rebooted, then re-created it?
You might also want to try the User Profile Hive Cleanup Service. Some people have reported success with that.
If indeed the size of the system part of the local machine hive has filled up, then I don't think there is a solution other than removing some software and running a second machine - be it virtual or physical. This would be really interesting to see; in all my professional career I have never seen a legitimately filled registry.