I'm just looking for a clarification on how the rules handle this. I can easily houserule the problem myself, but I want to make sure it isn't covered elsewhere already.
The extra IP for VR are available only because you are in VR mode. If you are not in VR mode, you do not have extra IP to worry about for physical actions.
You do have this p. 229 SR4
"Likewise, if you switch from VR to
physical/augmented reality, you immediately lose any extra
Initiative Passes from virtual reality that Combat Turn."
In SR4A p. 236
"Though Matrix Initiative is concurrent with physical Initiative,
any actions you take using your Matrix Initiative can only affect other
things in the Matrix (unless you are interacting with the physical world,
as when rigging or controlling a device). If you want to interact with
the physical world rather than the VR Matrix, you need to either go offline
or concentrate on your meat body and spend a turn using physical
Initiative (not forgetting the –6 dice pool modifier for physical actions
in VR)."
Though I haven't found much other text to address your question, the fact the penalty exists implies you can act physically while in VR mode. The question is really how many physical IP you can take, which is not explicitly addressed as far as I can tell. In my opinion I would limit Physical actions to the number of Physical IP during a turn, and you don't get to stack physical and matrix IP. e.g if you have 1 Physical and 3 VR Matrix, and stay in VR, you could get Physical- Matrix-Matrix, or Matrix-Matrix-Matrix.
And if someone says "It doesn't say I can't stack the physical and matrix IP" you can answer with "The book also doesn't say I shouldn't beat you in the face with it repeatedly with it."