It's a bit like the doctor's waiting room in here, only nicer. You come in with something that pains you, but when you leave, somehow it always gets fixed.
By trial and error I just found out that without PATH_INFO support you cannot use the plugins "Remove query string setting from processed resources" option.
I've just disabled this, and now those "bugs" are fixed.
I guess that explains the anomaly and gives the plugin's editor more to think about, than it does you.
And for my part, I don't feel like I want to start messing with the NginX configuration, unless I really need to, especially if you think its OK, doctor!
Terence.