I noticed this in my Zemmings Stream yesterday. After beating a level, when I started the next one, the replay from my last level automatically started playing out on the new level.
Tried to reproduce this (using LPO2), had no problems.
If you save a replay on one level in that pack, and try to load it on a different one, do you get the "This replay is for the wrong level warning"? If not, this would mean the cause is that all (or at least several) of his levels have the same level ID, usually as a result of creating a new level by using "Save As" on the old one and clearing it rather than using the actual "New" option; and it is something zanzindorf will need to fix (this fix is as simple as opening the offending levels in the editor, clicking the "Reset Level ID" button, and saving again). To be sure, test this using the two levels you encountered this problem between.
I should work on something to prevent this issue in the future, as aside from this issue, multiple levels with the same level ID can also cause problems with the mass replay tester, and the Replay Manager in Flexi Toolkit.
I haven't investigated whether that is the cause here or not. Will try and do so later today.
However, I'm going to implement a change to prevent Level ID-related issues for once and for all; by making Flexi refuse to build an NXP while a level ID conflict exists. I should probably look into making it automatically change the level ID, too. Ideally, this should be in a way that the same position in the same pack will always give the same ID, for people who re-import the level from elsewhere after modifying it rather than editing the copy within the Flexi folder itself. (However, the proper fix for this would be "Give the level a different ID in the first place", not "Rely on Flexi auto-fixing this problem", so I don't want to put together anything too elaborate.)
I'm still not noticing this happening in any case other than with duplicate level IDs (which the new version of Flexi will prevent), so since I haven't heard otherwise for this case, I'm closing this topic now.