This problem was caused by a large code reorganization that occured with v1.01 beta 4. Luckily, there does seem to be a way to correct this.
Delete the x:\Program Files\SharpStats Personal Tracker folder
Move all of your archived hand histories out of the [My] Documents\SSPT\Archive folder back into their respective import folders
Delete the [My] Documents\SSPT folder
Install the latest version of SharpStats (v1.01 official at this time)
If you are still having issues, please post a bug report in the forums.