I have been playing with this for a few days and have found a few things that are perhaps underdocumented and which might be helpful...
First, subpanels work great! Very cool indeed!
Second, there are a couple concepts that you need to wrap your head around. To begin, even though it looks like you are making calls to the subpanel VI you really aren't--you're just observing it's front panel. This is purely speculation, but I wouldn't be suprised to find out that the technology underlying subpanels is very similar to that which drives the remote frontpanel capability in LV.
This distinction becomes important when you need the VI making the subpanel calls to actually interact with the subpanel VIs (i.e. pass data back and forth, reference one another, etc). The examples that ship with LV show making calls using an Open VI Reference call to get a reference to the target VI. This means that the subpanel doesn't know it's be accessed as a subpanel, as a result the "calling" VI doesn't appear in the subpanel's call chain.
Because the appearance of the subpanel VI's front panel was psychologically stronger that the fact of how the code was connecting to the subpanel VI, I was initially fooled and reported it as a possible bug--after all it sure seemed like I was calling the other VI. But it now seems that this is the proper behavior given the type of reference opened to the subpanel VI. The program making the subpanel calls (if that's even the right term) was connected to the subpanel vi on some level, but it wasn't linked to it in the programming sense, hence its absence from the call chain.
If however, you do a call-by-reference, in that case you are actually linking to the subpanel vi so you can pass data through connector panes and the call chain shows the VI making the subpanel connection. As you would expect with or without a subpanel to provide a view of the front panel.
Hope this helps anyone else working with this functionality. I'll keep ya'll posted if I come across anything else that might be helpful.
Mike...