Version:           3.2.2 (using KDE 3.2.3,  (testing/unstable))
Compiler:          gcc version 3.3.3 (Debian 20040422)
OS:                Linux (i686) release 2.6.7

If I have several konqueror windows open that use a shared instance - so I opened them via the "New window" function (actually using mouse gestures, as that's the default there).
If I now do something that requires a little notification/alert window to be opened this window often gets open in another window than I'm currently at.
So if I delete a file the "you sure?" window appears on a konqueror window that has been in the background - bringing it into focus.
I guess it's pretty much related to the issue pointed out in another bug-report where new authentication windows are not allowed/visible across several shared-instance konqueror windows until the first one gets closed.

I know I can circumvent this by changing the mouse gesture to open a new instance of Konqueror. That would prevent a single crash closing all opened konqueror windows to close as well. But that's not the default and this issue should not be yet another reason (beneath the crashing issue) to not use shared instances.

Regards,
Chris