Inkscape strange printing errors

Here's something new. While preparing to have a go at some double-sided toner-transfer pcbs, we used "old faithful" ExpressPCB to create some layouts and printed to PDF (using CutePDF).
Then loaded the images into Inkscape, and flipped them (since we're making boards for SMT components, we have to flip the image so that it transfers the right way around)

So far so good.
But when printing from Inkscape, the actual printed paper doesn't quite look right.

At first glance it appears that some of the tracks are missing. But when you look a bit closer, you can see the tracks are there - just really faint/thin. So Inkscape is using an incorrect stroke thickness. But more than that, it's also lost the white background that isolates the trace from the filled plane.

But if you look closer still, even if the tracks were the correct thickness, and were drawn on top of even thicker white lines, they're not even in the right place!

For some reason, Inkscrape has shifted some of the tracks about 5mm over to the left.
I've stopped calling Inkscrape names like, well, erm InkscRape, and even Nutscrape (which the stupid python-based export plugins fail) because it's been pretty good of late. But something is definitely not right with the printing.

Onscreen everything looks just fine.

It just looks like Inkscrape is, once again, screwing stuff up!
The only way I've managed to get a decent print out so far is to select the boards, export as bitmap at 600dpi and then print from another application, to get the boards to come out of the printer the right way around.

It's do-able. But what a pain!