CPFC1985
Just a stab in the dark, but would screensets being locked affect this? Still getting used to Sonar here (previous Cubase user) so not sure if I'm talking rubbish.....
I think the answer is in the screenset. AFAIK, you will always be using a screenset, whether you selected and/or defined it yourself or not, so changes you make to your view will not be saved for next time unless you have unlocked the current screenset and locked it again so it's "up to speed" on the latest situation.
Before screensets, IIRC, the session would be reloaded as saved with the project the last time, but now we have screensets, you need to make sure your screenset has taken your current view on board to get it back again automatically next time. Otherwise, the project just uses what it finds in the (unchanged) screenset.
How many times I have hidden the Metronome and Preview buses only to see them back again because I didn't "inform" my screenset.