Sorry, you are spinning your own wheels. But clearly it is something in your data — it is not random and occurs in the same spot. We have no doubt you don’t know what it is, but your description (while colorful) doesn’t really tell us much.

Best guess: (based on little to no info about the data)...
Perhaps you are applying play effects that offset the timing... making for an unclear transition between Scenes. For example, if you are time shifting some of the data so that what you think is a 12 measure Scene actually extends the data beyond the end of measure 12... this loops fine but causes a glitch when not properly finalized.

If you are applying realtime Play FX, make sure you Normalize Play FX before attempting to flatten them into a linear Chain. Normalizing the data creates (prints) an event rather than simply offsetting the data.

I have not run into this myself (and I purposefully try to make all the mistake users might stumble on... ) But you’ve given something new to test...

Are you Clock shifting data with the Pattern Play FX?
If not, study your data in the first Scene does it loop properly by itself? (Most likely yes)
Does Scene 2 start cleanly when you just play beginning with Scene 2?
We’re there Arpeggios involved?
If yes, what procedure did you use to transfer the data to the Scene?

Alternate offline Solutions
Save Scene 1 as a .mid file export it to a DAW (or your ES) and look at the events in measure 12
Save Scene 2 as a .mid file export it to a DAW (or your ES) and look at the events in measure 1

Your trouble will, likely, reveal itself. Maybe you are applying too much Aftertouch unnecessarily (a problem that many heavy-handed players run into) if the Part is not set to use the Aftertouch, remove it

Hope that gives you a clue. Let us know.

Ok. Thanks. I'll try some of that.

It's a simple piano part for 12 bars then the second scene is the next 17 bars. The only effect I am adding is the sustain pedal. Nothing fancy, just 4/4 time signature. I'll look at the data tomorrow, if I get the chance. If not, then Saturday at the latest.

Sustain pedal!!! That’s a likely candidate for trouble.... check that every cc64 On message has a cc64 Off (0) message prior to your Scene end. Without even hearing this, you can understand how this can cause notes to extend past the end of the Scene (same as clock shifting notes into the abyss would do).. I think you’ve found your answer... (I’ll place my money on this as the culprit).

Remember: MIDI messages persist... it’s like a Newton Law of Physics but for MIDI: A MIDI cc message will change a parameter Value until another message of the same type acts to change it.
When you reach the end of Scene 1, if Hold 1 (Sustain) is still On, the Scene can’t officially end!

If, when recording into a Looping Pattern Scene 1, you let go of the sustain pedal a few clock ticks late... the cc64 Off (0) event winds up back in measure 1, instead of at the end of measure 12... Conversely, if you recorded with LOOP set to Off, and let go of the pedal after recording officially stopped, then the last message received by the tone engine was a Sustain On...

This is a common issue for some (until you become aware of it). If you step on the Sustain pedal before the Pattern goes into record, the cc64 message is not documented in the track data, if you fail to release that Sustain pedal before the last clock tick of the Scene, you wind up leaving a bunch of notes hanging over the edge. (Recording to a Looping Pattern requires the same skill as a child working with a Coloring Book... all your crayon coloring strokes must fit neatly within the lines defined by the “Length” setting.)

Let us know.

I agree, Bad Mister. I think that I had a similar issue with the Motif. I have a heavy foot (to go with my fingers). I was so frustrated, though that I wasn't seeing it. I ended up recording the entire song in Song mode. Took me a few takes, but I had to get closure and move on. I'll go back that Pattern and check it out after the weekend. This is all beneficial, though for future reference. I'm sure with the amount of music I'm producing I will run into these issues again. Thanks for all your hard work here - now and in the past. I've been a fan since 2005 when I bought my Motif and was on the Motifator forum looking for similar advice. Now THAT was a manual that was messed up....