<...snip...? (Bob, are you doing something unque to that piano track in your midi?). <...>
No, nothing unique.
It's a BiaB sgu.
I entered the chords in the BiaB matrix. C in bar 1 -- F7 in bar 5 -- C in bar 7 -- G7 in bar 9 -- F7 in bar 10 -- and C in bar 11. ---- repeat 6 times and a C on bar 13, the ending. Then I chose a style.
Every chord was entered on the first beat of the measure with no pushes, holds, rests or anything else that may be optional.
It's the most basic 12 bar blues progression - without even a turn around. Nothing fancy at all. In the song setting button, "Allow Realtracks substitution based on tempo" is checked.
Have you tried more than one Realtrack substitution? If so, does it exhibit the flawed results with every Realtrack you tried?
Note: I made this file on an old version of BiaB. I do that to make sure they run on older versions. Since BiaB has excellent backwards compatibility of sgu (and other) files it should play on any version of BiaB still out there.