Hi,
Thanks for the post. Here's what I think is happening.
The track you've got has time data, right? TopoFusion tries to improve the total elevation gain number by excluding segments that aren't considered "moving". It can handle simple reverses (it checks for whether time is before or after, between points), but if your file is a merger and has mixes and matches of time and no time data, reversing can goof it up.
Two things to try:
1 - Strip all time data from the file (reversed it doesn't make much sense anyway)
2 - Use the Climbing Analysis dialog -- there is an option to turn off checking for moving time
Hope that helps.