I suppose we are all talking about PT10.0 here. I've seen the bypass bug in my mixes as well (just didn't have time to investigate and manually edited the breakpoints).
I almost never use command-alt-/ btw, but use (punch)preview instead.
I've also had quite a few issues with automation not playing back, which is a PT10 issue in another thread, but since Avid replied here I jump on it
Often I get the feeling that these issues might have to do with de-activating and activating tracks in a session. I also mixed a project in 5.1 recently, where I used native processing on the source tracks (I tend to stick with TDM for everything). This also gave me a less confident feeling during the mix (more ticks and clicks upon stop-starts while monitoring through input-rec stems, than when using TDM only processing). I wonder if the automation problems surface more easily on PT 10 Sessions with native processing enabled or changing a bunch of tracks from TDM to Native, as I did with this mix. I imported tracks from HD2 and HD Native PT rigs, but always made sure the source and destination tracks for imports had the same processing (being TDM or Native). This to avoid the famous other bug from Frank, where automation suddenly can't be copied anymore between tracks.
Generally I feel that PT10 has great benefits for editing especially large sessions (Memory management is much better, Disk caching, 24h timeline), but on the mix side PT10 scares me sometimes. Also the D-Control implementation was best at PT8, became slower with PT9 and lost features with PT10 (plug-in learn stuff and CF plugin things)...
Sorry to hi-jack part of the thread, but I hope some insights might help troubleshooting.
Greetings,
Thierry