Those bugs are known, and in the bug tracker, as far as I know. As far as visual display bugs in Pd-extended, I'm not going to look at those until I start working on Pd-extended 0.43 and incorporating the new GUI. But patches are welcome if anyone wants to try their hand at that beforehand.
The code in pd.tk that makes the scrollbars hide is based on "pack forget", search for that.
I looked at that but still cannot find the culprit which is responsible for relocating the window upon restore... Will keep searching...
Many thanks!
ico