I've been working with M050 for about a month now and haven't experienced any of these issues. So far, I've found M050 to be pretty stable (knock on wood).
I agree with Gareth that checking if the problems persist when APTCUSTOM is set or not is a good place to start.
SPR 2258382 is fixed in 6.1M060.
The issue began in 6.1 M040
Iso, cgm or pvz graphics when visible in the Arbortext Edit window cause a delay in displaying keyed text, if the graphic is styled hidden and then emitted as generated text.
Workaround is to turn off generated text.