Hi Jack,
This won't help I'm afraid, but I can confirm I have seen the same behaviour. I think the reason is that IXApplicationActions 'assume' they will only work on designs or buildlists when no design is open. So they appear on the context menu of objects in the project browser. This was probably the original thought behind IXApplicationActions, but many people use them simply so they can make edits to designs other than the active/open design. I think there should probably be an additional value for IXAction.Trigger to allow the user to differentiate between the design context menu and the project browser context menu. Perhaps you should create an IDEA for this? (Mentor Ideas for Capital & Vesys)
Unfortunately, I couldn't find any workaround.
Simon