So to make sure I am understanding this correctly, if I type in /console reloadui after each boss it will save all the information even if i am suddenly disconnected from WoW?
Oh okay. To be sure, make sure your wow client isn't crashing, you aren't disconnecting suddenly from WoW, and you aren't using Alt+F4 to close WoW quickly. All of those will lead to data loss. Also make sure you're closing WoW before uploading.
I always recommend having more than one person in the raid running the GRSS mod precisely for this reason.
Also, if you want to force the mod to write to the hard drive, you can type /console reloadui whenever you want to do this.