If it is happening to others, this can be very problematic. When I used to record rap/hip hop, we'd stack the heck out of vocals using just clips. If I had to delete a section, all was great because I would select the section across all tracks, delete the hole and all would still be synchronized. With this bug, you got a heap of trouble. Think about it.
 
Maybe I'm missing a setting or something. I know "Options|On Stop Rewind to Now Marker" gets selected every once-in-a-while and I have no idea how it happens. Errant keystroke or ghost in the machine/software.

What if prior to doing your deletions you bounced the track to another track and did your editing there? That would cause data to be present even in the silence (in other words, no clips at that point - it's all one long clip). Then, you would always be selecting part of the track with data. 
 
I realize it's more work, but if doing it makes it so that the cutting and deleting the whole works, it might help until you find a different tool or workflow that is better.

mcdoma,
 
Just checking, does Sonar operate the same for you as the scenario described above? If so, its a bug in the latest release or a change in functionality.
Sucks when they screw up a great product.
 
 

Have you tried grouping all the tracks before you cut?  I agree that this inconsistency is something the bakers should correct, but in the mean time, anything that can get you back on track might be helpful.

Thanks all for your help and suggestions. If the folks at Cakewalk don't get back to me, I'll start a thread of its own to see if others encounter the same issue and get this bug (or functionality) addressed.
 
wt

Still buggy.