I ended up downloading the latest version of Quartus (version 7.2) as I was running version 7.0, uninstalled the old version and installed the latest.
This is how I fixed the problem although thats one problem down, it would seem now it doesn't connect to the JTAG chain over the USB blaster and i'm starting to think this board I got as a sort of employee hand-me-down has had it; that or the USB blaster is on the fritz.
Anyway, i'm tempted to format this computer and start from the very beginning; hopefully that'll have every single issue sorted out.