I may of found a temporary solution to this Madness. I to purchased a JVC HD-200ub and I was lost on why the hell this was happening and why nothing was being done by JVC or FCP to fix it. There is no rhyme or reason either for why this has worked, so I also have and SONY HDR-FX1 and I just thought to myself try the SONY HDV FIREWIRE Capture Control Preset and low and behold it worked with the JVC 200ub capturing with just the HDV capture preset. I logged the whole tape from one in point at the beginning and one out point at the end of the tape. I captured everything like it would normally with the sony with actually only breaking the clips at start/stops that occurred when shooting. No Randomness or 6 sec clips. I encourage everyone to try this but I am not 100% that this is a cure but I will see what happens as I continue to capture this way.
Good Luck!