Well, after some time and work the follwing is now the situation. I re-installed WB after uninstall, removed everything etc. Even removed any registry entries. Loaded 4.5F and then applied Pearle... skin. Recolored it and saved it as a subskin. Used per application for IExporer and it worked. Then copied my skins back to WB, deleted all .WB$ files, applied my current skin OpusOS, user Per Application on a recolored OpusOS for IE and, kaboom, it did not work. Nothing got skinned in IE, no titlebar visible.
So opened SkinStudio, opened a recolored version of OpusOS, saved it as a new seperated skin in its own directory. Then applied it to IE with per Application and, jippy, it worked. Seems like there is an issue with applying a subskin from OpusOS. The problem stays with subskins on OpusOS, even with the standard subs such as Olive or Deep. Resolving this now by saving my subskins as Normal Skins in their own directory.
Still think there is something wrong with WB, maybe it happend when I got SDCZIP.DLL errors (many of them) trying to restore WB after I installed 4.5d.
I will leave it as is for now. If Stardock wants ant contact to what happed etc., please contact me.
Thank you all for the replies.
Regards, TCM