Yes that might be the problem. Is this an ASUS P4C800 Deluxe or similar motherboard? We have had seen trouble with the ASUS on board Firewire. Direct M2T capture will function as the system has no work to do (you will find HDLink in M2T mode works also), but the CPU load of conversion can cause some poor Firewire implementations to drop packets. Contact support they know their stuff.