FCP Send to Motion - clips missing in Motion

I have a sequence I'm sending to Motion for tweaking and rendering. The FCP sequence has Templated transitions at chapter markers (templates I built in Motion) that work fine in the sequence. When I send the sequence I don't get the option to embed the Motion transitions unless I select all the clips in the sequence first - when I do that the Motion project only contains the first transition - none of the other clips in the FCP sequence appear. If I send the sequence from the project bin then all the clips arrive in Motion, except for the Motion templates.
A few other details. The FCP sequence is a chopped up screen recording session at 1024 x 768 in the Animation codec. All the clips have been conformed to 29.97 and play fine in FCP. I'm sending them to Motion as they are intended for 640 x 480 MPEG on DVDs. Some of the clips are time remapped in FCP and play fine but render terribly. Motion does a great job of scaling and time remapping the clips (unlike FCP) otherwise I'd just render from FCP.
Anyone have a solution?

Thanks Peter,
I can't find anything in User Prefs that would apply. After pushing the Send to Motion button in the "Export Selection to Motion Project" pane, if I leave "Embed 'Motion' Content" selected, it fires up Color. If I deselect the check box, and leave the clips as is on the timeline, it fires up Motion. It seems like an XML transfer bug. But I seem to be the only bonehead getting it. Which suggests user error.
Thanks again,
Bear

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