As I suspected, the startup preferences are stored in the registry.
It is likely that windows 10, pursuing the same lockdown techniques as OSX, is not allowing Pd to write to the registry. Google might get you further than this forum.
Everything..... paths, startup options, libraries to be loaded, audio and midi options are stored there.
If you cannot load libraries, or save your settings then that is because you cannot write to the registry.... it's part of the same problem.
I can post my settings that you could paste into your registry (and then modify) if you wish.... obviously at your own risk!........ but first.....
You can right-click the folders in the registry and change permissions.... which should be a zero risk.
Open Regedit and find the key folders listed below and check their permissions.....
You might need to open regedit with admin permissions.
You could also try opening Pd with admin permissions and trying to install cyclone and set paths, but I think it is wish85.exe that accesses the registry.
Vanilla and Extended preferences are stored separately in the following locations (Windows 7)....
This one twice...... probably last known good, and?
HKEY_USERS..."long string" ... Software\Classes\VirtualStore\MACHINE\SOFTWARE\Wow6432Node\Pd(and Pd-extended)
The "long string" will be different to mine on your machine.
@LiamG The garbled paths can be corrected and saved again....... which usually solves the problem.
That seems to be particular to Vanilla.