I've spoken to a rep, and he told me something that I think relates to all of this. he said the altera-made usb blaster is a piece of **** and has a bad signal that gives many people problems, and to always use terasic's cable instead.
This pretty much mirrors post# 2, "The real story is that you CAN connect the JTAG pins via pull-up to 3.3V, but it is not recommended because the overshoot caused by the download cable may damage your FPGA. So if you are going to be really careful, go ahead and use 3.3V for JTAG."
But in response to that post, a few other people asked, "wth does 'be careful' mean?" It seems the answer is to buy Terasic's cable. I would also use 3.3V, since that IS what the IO banks are running at and are expecting to see, and 2.5V is just a work-around.