Sounds like you should do disk error checking. Run a command prompt with Administrator privileges and type in ..
ChkDsk /F
it will ask you a Yes or No question.. type Y for yes

That will look for and try to fix damaged file and folder names on a scan. And any screwed up dates too.

Is your computer clock set to correct date and approx. time ? That can be important.

This post was edited by mikie on Sat, Jun 28, 14 at 1:58

For the files that won't load into MP3 Gain, will they play if you open them with an audio/media program?

The files or the tags could be corrupted. Can you delete the problem files and then get new versions by re-ripping or re-downloading the music (depending on where you got them from originally) ?

Or, how about trying something like Foobar to do the Replay Gain analysis? Or, use something like MP3 Tag to look at the metadata?

Tried your suggestions and still no answers.

After trying a few things I discovered the problem was with the Folder name....after re naming the folders all is well.

Thank you