I didn't take time since the last post to work on this issue, but I decided to get back to work before yesterday.
I took a blank HD, installed the OS (disabled some PRG in the auto folder like et6000 and novacal) + Magic + Jinnee + Nvdi (Nova graphic card) and you what, no more issues with the windows display
So I back'd up this new C drive to a ZIP cartridge, plugged my usual HD, renamed the system folders (auto, gemsys, jinnee ...) and copied the new ones.
I kept the inf and other configuration files to not loose my environment, rebooted and all is fine, and faster (well, that is one of the goal of NVDI isn't it ?).
I back'd the C: drive again to be sure to be able to reinstall it if necesary.
I'm going to tune the auto folder a bit but I hope this problem is definitively solved now.
Thanks a lot to all who took time to answer this subject.