Oops, sorry
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I just went back and read the whole thread ... it's not entirely an Illustrator problem.
I don't have
that
much help to offer but ran a dcd for a couple years, at least. You are not seeing normal behavior. I can't remember if the dialog boxes of which you speak always opened in the center or not - both my channels displayed on the same panel - but I am sure I could move them around. They did not "snap back to center" at all.
Zo, you have more than one problem. Your Illustrator problems (empty file dropdowns and so on ?) sound like real Illustrator problems.
But the system dialog boxes, you've got something wrong. They should move and resize quite happily all over the screen, and from screen to screen even with a dcd.
And you can set those to start up at a predefined location by using .Xdefaults. The dcd just thinks it's one big screen. Use xdpyinfo to find how big your display is, then xwininfo to find the -geometry data for the window you want to control (after you size it and put it where you want it). Then put that info into whatever you use to start the program or into your Xdefaults and bob's yer uncle.
@ robespierre : was (probably) a bad font. Tried a couple others from the ol' OS/2 stash, converted 'em from pfb2pfa and they work perfectly. But there's no afm's in X ?