Set JRE to use Windows trust store, specifically the user's trust store

A keystore of type Windows-ROOT should work -- it should access the TrustedRootCAs portion (line in MMC/certmgr.msc, tab in inetopt.cpl) of the store for the current user. On my system, which is 8.1 Home with UAC at max, but not in a domain or workgroup and no policy changes (at least none I authorized), Java code is able to insert into Windows-ROOT -- BUT it does pop a dialog about "Warning: about to install CA cert blah blah this may be a security risk blah blah" which I have to click; if the process doesn't have access to the 'workstation' (display) I don't know what happens and it wouldn't surprise me if it fails. Confirmed with both my normal id (local,admin) and Guest (local,peon); as a standalone system I have no real computer account, only 'local machine' which IINM is actually LocalSystem, and the insert does NOT go there.

You could try instead Windows-MY which should and for me does access the Personal portion of the store for (again) the current user; for me that works WITHOUT the dialog described above. Personal is intended for certs with privatekeys that can be used to authenticate this machine/user to server(s) or recipient(s), and having in there a cert-only used to trust another system may confuse or even alarm your more knowledgeable users, but it does work for me.