I had this with MP3 tracks which played on the XDJ-1000MK1 without issue. It turned out that the files had stream errors. After fixing them the CDJ-3000 played them perfectly.
What file type are you trying to play?
In case of MP3, you may try to check them. I am using mp3val under Windows. It can fix the files.
The older player may have been a bit more 'robust' with corrupted files.... just my thoughts.