Tony,
I'm on 6.9/ OS 10.3.9 (yes, unapproved as of yet, I think...but I'm a rebel, man! I take chances!)
I reinstalled my OS because I thought it was getting sluggish, and truth be told, I didn't want to have to go back and look for 10.3.8 plus all the prerequisites...I just clicked on 'Software Update' and went for it.
Somehow, I'm thinking the problem isn't related to the fact that I'm on 10.3.9 if you're running into that stuff...by the way, same here.
I've been having a couple of other weird bugs for the last couple or three months:
1. If I'm laying down a midi track and I'm following the click, sometimes the click will stop even though the transport is still running; then all of a sudden the click will catch up in train-wreck fashion...I actually end up playing through it sometimes if it's only for a beat or two. If I'm tracking to a midi instrument, it can do the same thing.
2. Actually, it's been doing this for a year now; sometimes the 'play' and 'record' functions won't work no matter how you try to engage them; whether you running the length of a selection, starting from a memory location, or from the start. Also, when you try to engage 'play' or 'record', you can see the 'stop' button on the edit window and the transport engage momentarily...at the same time you press the 'play' button. To put it more simply, when I press 'play' the stop button lights as well as the 'play' button...and nothing happens. Nothing short of closing and reopening the session will fix it.
There's something else different about PTLE, though. A while back I installed 6 Gigs of RAM in my dual 2 G5 and I was still having to run my H/W buffer way up to run a good number of plugins (I usually run at 24/44.1 these days) but now it's always at 128 and I don't have to give it a thought. Even with a bunch of UAD plugins, which drag the cpu on PTLE. I also keep BFD ReWired in case I want to layer a drum sound, which is also a big drag on the cpu. Something definitely changed . Anyone else notice PTLE running more efficiently? I'm not imagining this.