This is very odd. A couple of questions...
1. What is the exact version number of Jemplode you're running?
2. What is the version number of the player firmware you're running?
3. Have you checked the box in Jemplode that says "Use Hijack When Possible"?
4. Have you performed the "FIDsift" operation on your player? (If you don't know what this is, then that's OK because you haven't.)
5. Does your player have two disk drives in it?
6. Are the problem files truly random, or do they share a common characteristic? For example, a non-ASCII character in the target file name, a non-standard file type such as WMA or OGG, an odd bitrate, unusually long comment fields in the tags, they all came from the same source, anything like that?
7. What version of the Sun Java Runtime Engine is installed on your PC?