i don't really know why, maybe some of the W32 experts can help out.
far from being an expert ;-)
but björn !
i would try this in your case:
(if you can afford it, uninstall any PD and GEM installations you have on your machine, copy personal patches somewhere else)
download a .zip package of pd vanilla (no installation process !) and unpack it on a different drive (not your W10 system drive, though). can also be an external harddisk
http://msp.ucsd.edu/Software/pd-0.47-1.msw.zip
also download GEM as a .zip
https://puredata.info/downloads/gem/releases/0.93.3/Gem-0.93.3-W32-i686.zip
and unpack it's contents manually into a folder inside your PD folder (normally you would use "extra")
when you start PD (usually with a batch file), you can try to load GEM with the preferences method or if necessary you have to point to the GEM.dll location from a batch file. i.e.:
[YOUR PATH TO PD]\bin\pd.exe -noprefs -noaudio -nomidi -lib [YOUR PATH TO PD]\extra\Gem-0.93.3\Gem
(at least that's my preferred method)
hope i'm not suggesting something too obvious, but that's the way it works alright on my machine (W7, 64bit). if it works on your machine as well, you might try putting your PD "portable" folder to a more convenient place on your system. but in general i prefer not to "install" PD, as i like to have full control over externals etc.
best
oliver