Oops. My bad. Apologies: I didn’t fully read your OP properly (did it from the cell phone).
So if I understand correctly:
Track x = Destination TR707
Track y = Destination Other stuff
When adding the MIDI Effect: Delay to Track y, then the unit receiving on Track x tends to ‘skip notes’, yes?
If so, the only thing I can think of is something I used to run into in the old days if Track x and y are on the same MIDI Port. Older equipment (for me at least) used to barf when it’d get too much MIDI data, even if that data was destined for a channel OTHER than the one it was supposed to be listening to.
I’d suggest testing:
Put Track x out from MIDI Port A and Track y out from MIDI Port B where the only data heading out Port A is destined for the TR707. If you cannot dupe the issue, perhaps the TR707 is getting overloaded with data when the delay is used (doubling or more of note data) even tho it is destined for a different Channel.
Like I said, this was an issue for me back in the 80s & 90s and the solution was using a Router & filtering the data (each unit would only receive the data it’s supposed to do something with).