Ok, looking through our bug queue, these are issues we've fixed in 10.2 or 10.2.1 (which we're working on right now, its not released yet). However, they're easy enough to work around by deleting a file
When ArcCatalog opens, the tree opens to one particular folder. Make sure there are no PYTs in that folder.
If there are any, move or delete them. You can find what directory this is by looking if the registry if you aren't sure:
HKEY_Current_User\Software\Esri\Desktop10.1\ArcCatalog\Settings\LastLocation
or
Try deleting the ArcToolbox.dat found here:
C:\Users\[USER NAME]\AppData\Roaming\ESRI\Desktop10.1\ArcToolbox\ArcToolbox.dat
(this will reset your ArcCatalog profile)
Hope one of these helps
Joseph: could you post your PYT here for us to look at? thanks