There are a few things that could be happening, none of which are common.
I'd take a look at the file in the "Climbing Analysis" dialog. There you can get the straight climbing numbers without either of the two filters that are normally applied:
1 - box filter. This smooths out fluctuations in the elevation recordings, which is much less accurate than lat/lon on every GPS system.
2 - moving time filter. It's possible your file has some goofy time data or that the threshold for what is considered a moving speed is too high or too low. This filters out elevation gain that can be accumulated when your GPS isn't actually going anywhere.
Looking at your file if you strip the timestamps from it you get 6,369 ft of climbing, which is perhaps too high? Maybe not. I would suggest going to file->preferences->units and changing "moving time" down to 0.1 mph, so that anything higher than that is counted as moving.
Hope that helps a little. Feel free to ask more questions.
