It certainly could be a conflict, and sounds like the most likely.
Only other thing I might be prone to check is the connection. if the
pins ...no wait the new ones are probably etched thin PCB contacts, twists even a hair in some ports....well that happens. Do the "troublesome" ports have adequate power, and your sure the jumpers are seated to power the device as it pulls more current than a mouse or whatnot.
Finally to help find the source of the problem can you (assuming you know what you are doing

and are properly grounded) determined how many if any of the ports are plugged in via internal USB cord/socket. I cant explain all the possible outcomes, but if there 1 or more you can do some troubleshooting. if a "good" port and a "bad" port are plugged in by internal USB cords, first swap them, then search for other available USB male plug-sets on the MOBO, temporarily use your media card USB cord to MOBO connection. I think you get the picture! and I guess if not, maybe I shouldn't be encouraging you to do this! I'm kidding, just don't know ya' and don't want to assist in destroying our computer.
One last USB RANT...ignore if you want to!:
(I don't know if this part involves your or not, but I will say this - big USB A and/or B plugs are okay...smaller is better....but tiny is quite terrible! Every USB drive or even the mini plugs are to small to hold their own weight and can pull and bend downward over time leaving you with a "da-da"......"da-da"..... "da-da".... syndrome! If I breath on some flash drives at the wrong angle I risk corrupting my files! what ever happened to the metal sheath that was thick enough to hold its own weight? )
Mike