If your computer has a 1394B (FireWire 800) host adapter, then older Linux kernel releases will try to communicate at FireWire 800 speed even when 6-pin FireWire 400 cabling is used.
To avoid this problem, either use only 9-pin FireWire 800 cabling or switch to Linux kernel 2.6.18 or newer. These kernel releases are capable of downgrading to FireWire 400 speed when using 6-pin cables.