Yea, I used to do the same thing as you.. but I quickly learned there were more negatives with loading from a save then there were positives. I then knew that I should start a new game every time.. and I did. But after a starting a few new games for mod testing, I grew tired of "Wake up.. you were dreaming.." and "Ahh yes, we've been expecting you..".
So I made the modTESTchargen to remedy that.
It's amazing the amount of time it's saved me.. I'm working on a version three now. Well, that's enough with the shameless plug, let's get back to the matter at hand.
Try testing your mod once you install mine and let us know if it still happens.