My experience is that built-in and PCI-based NICs are faster and more reliable than their USB counterparts. Although it's gotten better, I still am not a big fan of USB for some categories of peripheral. My rule of thumb is to prefer any connection over USB if it's something that stays plugged in and is in constant use
(i.e. a NIC). For some weird reason, USB doesn't appear to like being kept as a persistent port assignment. Can't prove it since I never did any real scientific testing. But it does seem as though many USB connections experience more problems the longer they're left in. Probably more a flaw in the design of the devices themselves rather than the USB spec. Many USB implementations are done pretty half-assed on the cheaper devices.
Sometimes switching the jack a USB NIC is plugged into helps. (I'd try this first.) Also don't plug a USB NIC into a hub. That often causes oddball problems. USB NICs should always be plugged directly into the PC on their own connection.
You could also try running one of those USB utilities that gets rid of "necro" USB port assignments to clean out any junked up settings that may be causing errors or overhead. Remove all your USB goodies, zap the assignments, reboot, then replug everything in one at a time to let the internal ports get reassigned.