I have a similar setup. (Yes, what now...)I usually boot into Trisquel in legacy mode, and when I need to use Windows I switch into UEFI mode. I've tried to get Trisquel to boot in UEFI mode by default, but most UEFI implementations these days are crap and only useful for booting Windows.
Are you sure booting into Windows in legacy mode is supposed to work? Before I installed Trisquel, my MBR boot code was all zeros. I don't think booting into Windows in legacy mode is supposed to work.
