I have the same problem on my machine at work; dual 4:3 monitors running XP 32bit. I have one row of panels locked in the default position, though I have no doubt changed which panels reside there, and have another bunch sitting off on the other monitor. I do the same thing in Indesign, but seem to have no issue there.

I don't seem to have the same problem on my home machine, which runs a single wide-screen monitor, Vista 64bit. I think it's hung on close a few times, but I just attributed this to random crashes (let's face it, both Windows and Adobe products do this a lot). I have two rows of panels; one in the standard locked position, and one floating.

My partner always floats all of his (and moves them all over the page as he works, so that I can't watch him doing anything without wanting to scream), and I don't recall him complaining of this issue.

What issue I do have is mostly unrelated, though it could be from the same section of code; in Photoshop, I can happily move any subwindows or images around on either screen. Illustrator and Indesign will not let me; I have to have images on the left, though it will let me put panels anywhere.