It's very strange that you can't track or stabilize a nested comp. Sorry but I think it's a case of user error. Have you tried open the nested comp in its Layer Panel and tehn opening up the Tracker Controls Panel, in that sequence. And evem then, from the Tracker Controls Panel, there is a drop-down menu to selct the source for the tracking/stabilization.
And creating a hi-con version for tracking is a good idea in certain cases cos it allows you to exclude information that you don't need while accentuating the ones that you do.
BTW, how did you manage with the averaging of your tracks?
Cheers
RoRK
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