I do not see issues with your SheepShaver setup itself. But there are, possibly serious, problems with the file system on your disk!
I usually notice issues with the shutdown process of the Mac. The pinwheel will spin constantly and the computer will not shutdown unless I hold the power button in for a forced shutdown.
That certainly is not normal, but I do not know this as a result of using SheepShaver. Do you wait long enough for the shut down to occur? It may sometimes take many minutes. A force shutdown could by itself cause file system problems, though rare since we use HFS+ journaled.
Now every time after I use SS, I reboot into terminal mode and will run sbin/fsck –fy which always shows the volume as having been modified.
When you see the message ***** FILE SYSTEM WAS MODIFIED *****
you should never be satisfied that all file system problems are repaired.
You need to repeat, and repeat again, sbin/fsck –fy until you get the message ** The volume (name_of_volume) appears to be OK
See also here: http://support.apple.com/kb/ts1417
Note that when you run AppleJack in auto mode, there is no way to tell if "disk repair" (fsck) has repaired all issues on the hard disk! See AppleJack documentation.
After this process, I run Applejack and tons of permissions requiring repair whiz by.
That is normal and does not necessarily mean that the permissions actually needed repair. If you want to discern between the normal report of a permissions repair after using your Mac for a couple of days without using SheepShaver and one after using SheepShaver in that period, do the permissions repair in Disk Utility with "Show details" checked. That will enable you to copy the reports and compare them.
However, at this point, I would be more concerned about the file system problems. Unresolved file system issues will inevitably become worse and you risk serious data loss. Make sure you have a good backup of all your important files. Then try repairing the disk with sbin/fsck –fy or with Disk Utility from the system install DVD until you get the message that the volume is OK. If the volume cannot be repaired that way, you could try third party solutions, like DiskWarrior. DiskWarrior can sometimes solve problems that Disk Utility (and fsck) cannot repair.
Finally: I never heard of such problems caused by the use of SheepShaver. The file system problems may be pre-existing and may become worse by using an application that writes large files to disk, like SheepShaver does. How much memory does your MBP have and how much free space do you keep on your HD?
You don't shut down your MBP while SheepShaver is still running, or do you?