Adobe Media Encoder may be the better tool for batch conversions. Give that a go.
If the option were there I would first go back to the original recorded media, with all the file structure and ingest directly into FCPX. Otherwise I have found that if I export to Media Encoder even after I select the ProRes option I have to manually change the resolution. ME seems to default to SD rez for me anyway.
In my previous system (5.5, but now in 6) I had created presets in ME for output to ProRes. I've not gotten around to creating them yet on our new/clean MacPro. There's a blog article on Adobe's site. You'd have to google it. "ProRes workflow in Premiere". I think that's how I found it. Sorry, I've lost that link since I updated the computer.
If this happens very often you could always purchase Prelude and use it to convert to ProRes.
I don't know about you, but sometimes as soon as I ask someone where my car keys got to, I find them right away. Same with this question. If I had just scrolled down the export window farther there is the setting window and from there PPr took me to ME which output the desired size and codec.
Thanks for your helpful replies!