I did a bit of guess and test on some different things and I managed to find a fix. I first tried deleting the original and recopying the file out. This didn't do much. The MOH audio still skipped. I then tried copying the old version back out. I switched the MOH file to the older version and that worked just fine. I finally tried renaming the new MOH file something different then copying it out. I changed the MOH to point at renamed new audio file and that seemed to work. I cleaned up the flash card and renamed the working MOH file back to the original name and everything held up fine.
I believe the CF card has a few bad sectors on it. The original location of the file on the CF was the issue. Simply deleting it and recopying the file placed the new copy in the same space on the CF card. Copying 2 versions of the same file to the CF card forces one of the files to be located on memory space that isn't affected by the corruption. This is just a guess of course.