I'm trying to figure out what the hell you mean? What is the glitch? You didn't explain well. You appear to be complaining about FTB's intended function? It's not well suited to custom mod packs as the auto update feature seems to override the edits you make. For example remove Railcraft (and BC) if you update the pack Railcraft will be added back. It's like this becasue the launcher has not been designed to scan your old instance for changes, it just DLs everything to the pack compilers specifications. This is done to maintain pack consistency for multiplayer, which is what FTB's strength lies.
If you don't like having things "dictated" to you, try to use a launcher that's purpose built for custom Minecraft instances which the FTB launcher isn't. I use MultiMC myself, in fact I use a pack that I started from scratch that didn't use a FTB pack as a base.
However some knowledge regarding mod compatibility is essential to get it working, I only recommend using it if you have boundless amounts of patience.