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

Thanks
Colin McGowan