Why do files drop out of WebHelp builds when they exist in the original project?

I am using RH 10 (upgraded early June 2013), Windows 7 and we support IE 9, Chrome, and Firefox.

I build my WebHelp to a WebHelpGenerated folder before checking it into CVS for my development to pull and place in our product.

My project has 1200 files.

I update a topic, save, generate, and lately the build has missing topic pages.

They display in the TOC, but the file is missing altogether and when I check the output View in RH10, it is missing there too, but the file is in the existing project folder. Somewhere along the way, the build is not picking up miscellaneous files.

In 2 of 3 cases, in my project folder, I had the original file and what I assume is some kind of duplicate file, that had a tilde symbol, for example, instructions~.htm. I didn't have permissions to do anything with this file, but after a reboot, I could delete the file, rebuild the Help and everything would be fine. In one case, I didn't have the odd file, but couldn't get the missing file in the build until a reboot.

Any help you can provide would be greatly appreciated.

Thanks