Good news, I didn't fry my charger after all. Discovered that I was blowing fuses because when I was trying to charge using the ciggarette lighter adaptor I was over loading the built in fuse! (dumb because I did that once before!)
Tried the charger this morning directly on the auto battery (with engine off) and it worked fine!
I would still advice against running your car engine while charging because the charger did act up and over charge some lipos, of that I am sure. And now with the engine off it is charging like there was never a problem.
I'm just glad now that I am back to having two working chargers again! In case I really kill one of them some day!
Thank again for everyone's opinions!