So I bet there are undocumented file size limitations lurking somewhere, wish I knew what they were.
The only PSB file limitations are 300K x 300K. But I don't think it's a question of PSBs being slow when saving...I think it's the Save in the background that is causing your slowness. In the CS6 Prefs under File Handling do you have the Save in Background turned on? Also under File Compatibility do you have Disable Compression of PSD & PSB files turned on?
What I think you are seeing (although 2 hrs seems way excessive) is that saving in the background is a background process that cuts the cpu cycles to allow further work and means saving is no longer "modal". This can be a good thing but it can also have consequences–it takes more time to start and execute a save.
For myself, I've found that the downsides of Save in Background outweigh the upsides and I really started hating the Auto Save. I'm not saying YOU should turn it off, but it's something you might want to test. Also, the compression for PSD & PSB files also takes extra cpu clicks–another factor in slowing saves down.