So if I get this straight:
you midi-sequence a synth… and send that synth back to your octa.
So you got a midi-track and an audiotrack.

While setting this up… you probably had hold-part of envelope of audiotrack on infinity.
while playing you turned this back… and nothing really happend… atleast you did not hear it straight away…
Now you turned off octatrack. some time later turned it back on…
and suddenly you do hear a difrence in the sound, because your octatrack starts of
with the envelope settings as what they where left at… (which is not infinite)

I am not claiming it IS the answer… but I would definatly recheck the hold/release envelope settings of the audiotrack eating the input of your synth…
I had simular experiences, but with attack of filter… Only really heard it after

  • reboot
  • when I stopped sequencer (first stop-button press) and stopping the audio-engine (dubble-press stop)

Enjoy…