I've seen the same behavior with Texas Hold'em and a couple of other games. It is like it has switched to another task and the task isn't releasing the processor for a second before it comes back to the game. May be because the processor is under powered for games.
Brickbreaker performance is horrible if you have any other apps active. Which really sucks, I like playing brickbreaker while waiting for web pages to trickle across to my frankenberry.
I have the same problem. I think it is definitley something with the track wheel even though it'll pause when I'm not even touching it. I hope after a week or so of breaking it in it'll go away. The tapwave zodiac had buttons that behaved bad until they were "broken in" as well.
Do you actually mean the game freezing or the game pausing properly, if it is that latter it could be intentional since the game's performance always used to suffer when there was radio traffic and rim might have tried to address this.
I've taken to actually closing applications rather than just backing out of them. Seems to help with the BB issue...either that or its mellowing with age