The actual video should have been 1 clip 39 minutes long... but in FCP log & transfer window I see 3 clips of 13 minutes each. That sux!!

It's a big problem because I shoot longer than 13 minutes all the time and I combine several cameras (that also shoot longer than 13 minutes) into multi-clips.

Is there something I'm missing? Is there a way to join these without re-writing the 3 files into a single file?

Have you read the PDFs for ClipBrowser2 or XDCAM Transfer 2.7 yet?
File size limit is 4GB as card is FAT32 formated. XDCAM Transfer joins them on conversion to .mov. Just make sure all BPAVs are mounted and selected in XDCAM Transfer and import all converts them.

I've imported single clips from 8 pieces without a hitch.