Back to unresolved, I've found a way to recreate it.
It's down to what chord you put in the first bar, first beat. For instance, use something like C5, C7, Cdim and the problem exists. Cm, Cm7 no problem, I haven't tried others.

Can anybody confirm?

Steps to recreate ...

Create a new song with 4 bar ending for realtracks. Just for simplicity make it 12 bars, use chord C throughout and 2x chorus. Use style "TEXROCK.STY w/2 guitars"

In bar two of the ending, everything is normal, chords are held.

Now change the chord to C7 at the first bar, first beat.
In the second bar of the ending, the drums, bass and guitar 1 all end normally. Guitars 1 and 2 carry on playing.
Make the song 1 chorus and everything works correctly again.

I've tried the same with 5, 7 and diminished chord, it's probably the same with others. Use these chords anywhere other than the first beat and all works as expected.