Found a couple of bugs with your programs, including a few game killer bugs
1. TShip editing, if you directly enter weapon/missle values into the raw data areas 18 and/or 24, your program will put .000000 on the end of the number. This breaks the game as the game will be unable to read beyond this (took me almost a day of examining the TShips file by hand to find this problem), and will only show ships in game up to the last ship that doesnt have .00000 at the end.
2. TCockpits editing, Same problem with weapons as the above when editing the raw data, but also it does the same thing if you enter the number into the info tab under "possible lasers". The problem is also that it is entering .000000 after the number. This also breaks the game as the game wont be able to read the TCockpit file and will default to the weapons listed in TShips for the turrets.
3. TMissles editing, this one is a simple bug your companion mod manager program does not recognise that TMissles can be edited with your TXT editor, and instead opens it with notepad or wordpad. Manually opening it using your txt editor works fine though.
Anyhow thought you might like to know

Its a really nice set of programs you made, and makes editing so much easier.
Btw incase anyone else runs into these bugs, this is how you fix them
1. Re-enter the numbers into the "possible lasers" and/or "possible missiles" in the "weapons" tab, or go into the "front lasers" and/or "front missles" tabs and alter the weapons list (add and remove a weapon or vice versa)
2. This one i think you can fix by going into the turret info tab and altering the weapons list. I fixed it pulling the TCockpits file out of its cat&dat file and manualy searching for and removing all .000000 entries with notepad
Lastly I hope I haven't necroed this post, I do not know if the author is still around or not, but I figured he may want to know about the bugs, and also this may be helpful to other modders who may stumble on these problems and not be able to fix them.