What kind of load are you putting on the card PCTC2? Try running something like Furmark and see how it does. I had a 6950 DirectCU II that would overheat in the vertical orientation in an FT02. Simply rotating the case 90 degrees so that it then sat on its face and the video card was in the conventional horizontal orientation caused the card to go from running at 100C+ in Furmark to about 80C I think. There's no denying that some heatpipe coolers don't work well in the FT02, the results are clear as day in the EXPreview article chedrz linked to. Not everybody will have problems, though, if you don't stress the card too hard it might not be an issue. For example with my 6950 it didn't overheat at stock speeds while running Furmark, only when the card was overclocked did the cooler seem to become overwhelmed in the vertical orientation and not be able to pull heat away from the GPU faster than it was generating it. Also if you just game on it overheating might not be an issue, gaming won't produce nearly as much heat as loads like Furmark.
The issue doesn't have to do with heat rising. The problem is that with certain cooler designs, after the working fluid condenses at the cool end of the heatpipe, it has a much greater distance it has to work against gravity to return to the hot end in the vertical orientation than it would in the conventional horizontal orientation. That's my understanding at least.
Twin Frozr is your best bet IMO OP, both the DC II and Windforce coolers have heatpipes that run the length of the card, which seems to hurt performance more in the vertical orientation. The Twin Frozr cooler performs just as good in the EXPreview article in the vertical orientation, though. I've also used an MSI 5770 Hawk in an FT02 and it seemed to work fine, even when overclocked/overvolted and running a heavy load like Furmark or Bitcoin mining.