As of CXOffice 5.0.1 there is still a problem between Quicken opening dialog windows and the window manager. Frequently, the split window (for example) will flash rapidly between a small square window and the normal-size window and will not stop or occassionally it stops with a non-resizable small window that is too tiny to be useful.
There is no guaranteed workaround but the choice of window manager seems to make a difference. Using KDE seems to produce more problems (such as interiminably flashing windows) whereas XFCE (and possibly Gnome) will flash, but more often than not do stop flashing on a correctly-sized dialog window. Sometimes multiple tries to open a dialog or opening other windows and then retrying the problematic dialog works, other times it doesn't. Restarting is also not guaranteed to work.
Update (XGL/Compiz): Since Novell released their 3D OpenGL-based window manager 'Compiz' I've experienced no problems with the flashing/resizing dialog. It seems clear the different window managers do play a vital role in how this anomaly exposes itself (if it does it at all). YMMV
