I've had good success with fax over IP in production. An error free network with minimal loss and jitter is key. Excessive delay, packet loss and jitter will definitely affect this type of traffic. I have no experience with fax/modem traffic over a microwave link, but I would highly doubt that this would work with any consistency.
This is likely due to the errors and packet loss that you mentioned. You might check with the carrier regarding these problems. Also, check you configuration to make sure that there is not a misconfiguration causing slips, etc.
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