Some thoughts/suggestions

[dflat]

I am using v2.8 on Mountain Lion and experienced these problems recently. I think it has been at this version for a while.
1. I have never set the number of times to 999 ( 12 max ). I think one time I saw it change while changing the Metronome speed i.e. it is being set to this number by a glitch in the app not be using the up arrows.

I will see if I can replicate this in the current version with the metronome speed. Thanks for letting us know.
(You would not have been able to create this number under 'normal' circumstances, but the bug produced it in a previous version. If you have had iReal b for a while, some of the 999s might have been caused back then and stored with the song at that time.)

2. Not a big issue as it takes a lot of times round for it to happen but I think it still does happen.

Is this when you do a loop or when you have a large chorus count do you know?

4. I am using the tool primarily for setting myself rhythm sight reading tests for my upcoming guitar exam so ideally Am7#5 ( which is one of the chords I am required to know ) could be represented.

This probably will not be useful, but you could add the Am7#5 as an alt chord above the Am#5, the lower will play as the player knows what it is, and you can glance at the alt one above.