I've just checked in an updated dialogs/object-properties.c which makes this dialog (ctrl-shift-f) transient. This means it always stays on top of the canvas window (if there are several, it attaches to the one which was current when the dialog was created) and minimizes/maximizes together with it.
What can I say? I'm absolutely astonished by how simple it turned out to be, and really baffled by the fact that nobody did it before. It's been in the Sodipodi programming tasks for ages, and it's actually just two lines of code. The difference in usability however is enormous. Judging by the fact that GIMP's interface, despite being almost universally hated, has never attempted to use transient windows (at least in the stable series, I did not try their development series) made me think that this problem is somehow unsolvable on linux - but no.
At least, it works for me (on KDE 3.1).
Please test the CVS HEAD with this change and report any problems you may have with this dialog (ctrl-shift-f). If there are none, I will make all other dialogs and the toolbar transient too.
And by the way, the dialog can now be closed by esc - please test this too, and if there are no problems with that I will change all other dialogs likewise.
Misc:
I made the zoom field (in the bottom right corner of the canvas) unfocusable, so it never steals focus any more. Now arrows should work reliably.
I also changed the treatment of keypad arrows - now they hopefully work both with and without shift (so far only in selector). Please test this and report any problems. If anyone can test this on Windows or Mac that would be great.