I presume you mean that you are adding a new Keystroke Action to an existing Mapped Key. All Keystroke Actions in the same Step of a Mapped Key get combined, not sent separately and sequentially as you might like. MiRai explains it really well here and then goes on to explain how to avoid this happening.

I'm not sure I understand your second issue and would probably need to see your ISBoxer configuration to work out what is happening. Also, which Key Maps (or do you mean Mapped Keys?) don't work in this scenario.

edit: video link to specific time