Support has managed to reproduce with the below steps, passed onto devs...
--->
STEPS TO REPRO:
1) New song.
2) Add an audio event (music clip of about a minute or something, doesn't matter that much)
3) After that event, add another audio event on the same audio track, give it a gap of a fews seconds or so inbetween events).
4) On keyboard keep left shift held down on your keyboard, left click (with mouse) on the first clip on the left, and then left click the following clip (still keeping shift held down. (MAKE SURE YOU SELECT VIA THIS METHOD AND NOT LASSO).
5) Right click -> Separate Stems
6) Click OK. Observe it takes two steps to process.
EXPECTED:
Audio created for both events in a folder (4 tracks)
ACTUAL:
Audio for just one event (4 tracks).
OBSERVE VIDEO BELOW:
Note the first go, which I stated "as you would expect" afterwards... well the clips on the right start late which is odd.
The second go demonstrates the issue I've written above.
Thanks!