I often haven an issue on Premiere with both audio transitions and straight audio cuts, the jump sounds fine when I play it on the timeline but some of the audio then cuts differently after I export, for example words might be cut abruptly or keep going too long in the export but sound perfectly fine when I playback the timeline, quite frustrating actually.
For big projects I now export just the audio until I get it right which often means "casually" try to adjust the cuts which now don't sound right in the timeline but do after the export. Anyone having the same issue?
This is completely a wild guess and may not apply to your situation at all.
Are any of your audio files MP3 format? If so, try converting to WAV files and replacing them. See if the issue goes away.
This is a wild guess. We don't know anything about your Adobe software version, computer hardware, OS, anything. SO folks can only offer so much in response.
Dell Precision T7600 (x2)
Win 7 64-bit
Adobe CC 2017.1 (as of 8/2017)
256GB SSD system drive
4 internal media drives RAID 5
Typically cutting short form from UHD MP4, HD MP4, and HD P2 MXF.