DavidG, I am sorry. I thought that most of what happened to me was because I was changing 2 different tech level requirements in each level of the weapon. I could see part of what you described though. Makes me feel better anyhow to know I wasn't totally losing my mind.
What you describe as happening when you modify a current component to make a new similar component was definetly part of the problem, and the Family Group putting the rest of the family on the bottom of the .txt file but not showing that in the Tree really had me confused.
I hope you are able to do something about this. It is so much easier to use your SE4Modder to make a mod. I straightened out the problems, in my mod that this caused, manually. It only took about 3 hours whereas it only took about 10 minutes to do using the modder.
Keep refining the program. It has excellent potential. Thank you.