The solution to this is to use the "Discard Trackpoints" feature. This happens often when you have One Second Recording turned on your GPS for a very long activity. The default setting is called Smart Recording, which only records trackpoints when necessary. I recommend that you leave your GPS on Smart Recording, but if you have already recorded an activity using One Second Recording, Please use the feature to discard track points.
The option to discard trackpoints is in the "Add / Remove Track Points" area. You can discard up to every 10 trackpoints. See image below.
If you are combining a TON of files, you may need to shrink each file one-at-a-time using this option described above... and then you will need to merge all of the shrunken files using my tool. This technique also helps in case your files are too big for my tool to process at once.
Here is a discussion on other strategies for uploading large GPS files.