I've not seen this though I don't use the "My Database" feature of the software nor do I use the "Factory Database". I don't see these things as time savers. My preference as with the prior Pronto editors is to use dedicated devices for each IR codeset I need in a given PCF. That being said, I did test the "Save to My Database" feature during the beta test and never ran into the problems you've described. Quickly going back to test again today things still remain problem free in this regard.

As an aside to your particular issue I thought I'd list some of the quirks I noticed right off the bat with the My Database feature of the software.

-If you delete an item under "My Database" the brand name still shows up under "My Database Quick Access" when it should not. This is in cases where there is not additional items under "My Database" remaining for a given brand name.
-When choosing the "Save to My Database" option the "Identify Equipment" window comes up with drop down lists for brand, device, and model. The items found under the brand name drop down list don't show in aphabetical order. Instead they are listed in the order you've added them to "My Database" which I can see being a real pain as your "My Database" grows.
-Once saving a given device to "My Database" there is no way to go back and edit the device category name you've created or even delete it entirely.