While theme support had several tickets logged on Cmd 3.0.x I am not certain this is a bug or not... To support Neptune in Cmd 3.1 we had to do a lot of work on the slicer and fixed many limitations there. Cmd 3.1 will support 4.1 apps for GA (due very soon now) so if you are not planning to move to 4.2 then you could see if the new version works better for you.
I suspect you had to add to the shortcuts and/or manifest for your theme? In 3.1 we have documented and fixed issues with this API so that you can more easily extend these with new UI's or components.
Again, the current beta of Cmd 3.1 does not support 4.1 but we will fix that. When a build of Cmd 3.1 supports Ext JS 4.1 I would be glad to help you work through any remaining issues.