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For anyone else having this issue, we found a workaround. When the device was unplugged from the USB port, we'd need to reprogram it or change the baud rate a couple times. I noticed the devices worked fine when using minicom and other serial programs, so we looked at the source of these programs to see what they're doing. minicom "resets" the modem by setting the baud to 0 and back. We just made SerialClient.py do the same:
self.port = Serial(port, baud, timeout=self.timeout*0.5)
changes to
self.port = Serial(port, 0, timeout=self.timeout*0.5)
self.port.baudrate = baud
time.sleep(2.0) # give usb chip time to reset
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