I'm posting a resolution that we found to our throughput window in Visual 9.0.1. I recently found out that other admins might be running into the freezing throughput window after running the allocation utilities.
The Preference setting information is as follows:
Section: Throughput Window(tm) Entry: Soft Allocations Delay(milliseconds)
Value: 3600000 (note this value is in milliseconds so every 1000 milliseconds equals 1 second, the 3600000 is equal to an hour, though the value can be set as desired)