I opened a project, that I began recording on C5.5 and then edited on C6, and all the group tracks settings are lost.
All the plugs disappeared.
My luck is that I’ve another backup from 10 minutes after that file…
But now I’m scared… Brrr 
Pity their ain’t track presets for groups.
I (personally) don’t think it’s a bug, but more Steinberg have likely built in support for Track Presets on Group (busses) Tracks.
Well if you did a mixing with many plug-ins and rountings and then next day you open it and the plugs disappeared and the routings are gone.
That is what? Black magic??
I had this issue sometimes on C5, before C5.5 on OSX too…
And then in C5.5. they corrected it.
yea I just got Cubase 6 as well and no sound was come out as i looked i noticed nothing was getting to the group busses after a bit of messing around i noticed if I unassigine the busses the re assigne them the Group pan would change to na new look and the sound was back and working. I think this is just a change in the new cubase 6.
Later I can send the project without the audio files to Steinberg.
I had another project that change the FX. Plugs and panning disappeared…
Now I’m going to use C5.5 again…
Disable your plugs before exit.
What’s the email to send the problematic project to Steinberg?
info at steinberg dot de
Finally they answered…
Send an email to Steinberg Portugal representative…
Nice one!!! 
What they can do? Forward my email to them again?
Till now I didn’t got any reply from any mod or Steinberg…
Today I had the same problem on a song made on C6 on Windows and then when I opened it on Mac and made just some editings, save 3 times with different names and all the 3 files have the same problem:
- it takes more time to open (more than a minute-9
- some groups loose the outputs and plug-ins
- fx’s loose the outputs and plug-ins
I created a new template for C6, just FX’s chains, (presuming that would be some problematic issue with my C5 template) and then record a song.
The problem occurs again, when I open the project it takes more time than usual and there’s a FX’s slot that disappeared… It had Mono Delay at 1/2 and a Studio EQ. The routing for this FX is gone too…
Another songs with the same problems!!!
After mixing, I had to redo something and when I open a song, it took many time to open it, then some fx’s disappeared and the other’s change their positions on the channels, for example, reverbs became delays…
Brrrrr 
I tried open it with C5, and the same problems…
Bump