Disclaimer: I don't own a Pod 2.0, but I didn't see any way (in the online manual) to enable a soft THRU setting. That is, whatever comes into the MIDI In jack can be passed on THRU to the MIDI Out jack. The reason that your alternate routing works is that (I suspect) you have SPACE set to [utility] -> MIDI -> OUTPUT -> THRU (rather than XMT).
With SPACE first, the Pod is at the end-of-the-line for the MIDI signal. The MIDI OUT isn't needed. If the POD goes first, the MIDI signal stops there (internal to the POD). Again, wait for verification from an actual Pod user, but that's my guess.
I'm wondering if your pedal layout can remain the same, using the working MIDI routing, and the addition of a longer MIDI cable (SPACE MIDI Out -> Pod 2.0 MIDI In jack)?
