It was a dpi problem from Illustrator. Apparently the SVG export (used for the board shape) there uses a different setting than everyone else. So the Fritzing chaps had attempted to tweak their system to accomodate but had missed this bit.
Turns out the drill file probably isn't an issue. ViewMate won't import it but it seems fine elsewhere.
And the board mirroring is probably ok since the silkscreen output is on the bottom layer, so if viewed top down it would probably appear flipped.
I've sent it off through BatchPCB so will let you know in a month whether it all worked. 