Most likely this issue is caused by files being recorded with a VBR (variable bitrate) that do not include the xing tag in the file header. Some encoding software programs do not include xing tags. When you play a long VBR files, Pocket Tunes has to "guess" as to the length (time) of the file, and most often that guess is wrong unless xing tags are present. To guess accurately we would have to scan the entire file which would take an unacceptable amount of time for most users.
This situation should be easily resolved by re-encoding the files at a set bitrate, or if you are comfortable editing tags, add and enable the xing tags in the files. The easiest method would be to re-encode at a static bitrate, obviously.
Should this somehow not resolve the issue, you may send us one of the files for testing if you would like to do so.