@ilpoj It could be a widows10 update.
tcl ........ pd_guiprefs.tcl performs the read/writes through the "registry" object.
On a 64-bit system 32-bit apps write to the "VirtualStore" in the registry.
What is 64-bit and what is 32-bit in Pd and Tcl/Tk?
Maybe it's writing to one and reading from the other?
Tcl........ Tcl 8.6 recommended........
https://stackoverflow.com/questions/31432958/tcl-unable-to-read-variables-of-32-bit-registry-hierarchy-on-a-64-bit-machine
Widows........ Microsoft intend to bin VirtualStore and force app compatibility.....
...... have they just started this process?
https://msdn.microsoft.com/en-us/library/windows/desktop/aa965884(v=vs.85).aspx
Other software identical problem.......
http://knowledgebase.progress.com/articles/Article/UACvirtualisation
Pd_guiprefs.tcl on-going work....... 16 days ago.... maybe time to post a bug?
https://github.com/pure-data/pure-data/tree/master/tcl

Again..... Tcl 8.6 recommended.......
https://community.activestate.com/node/11350
and....
http://www.tcl.tk/cgi-bin/tct/tip/362.html
David.

@ingox Thanks, but when I add -prefs, it doesn't actually open Pd at all.

@whale-av Thanks for the info and the links! I'll have a better look at these if this becomes an issue - so far it's working fine, with the -path in the shortcut.