Thank you Azrael,
The issue was the CDE windows settings of "Desktop Controls; Window Style Manager" a setting of "Allow Primary Windows On Top" needed to be de-activated for the pop-up windows to stay on top.
We have recently upgraded from Catia V5R16 on Solaris 8 to Catia V5R18 (SP4, HF30) on Solaris 10. Ever since the upgrade, Catia sub-windows (fly-outs, pop-ups, whatever you want to call them) do not stay on top. When an item is selected from the main window, the pop-up disappears and the main...