Yea, read that thread. Also look in the mods forum for info/pics from Kered on going lipo with his XS and GT. Like he said, if you go lipo you'll never look back.
Just the same, on your problem. Can you be more clear what's going on? Did you take apart the stock rechargable pack and then rebuild that with new cells? If you did, even if the capacity of those cells is much higher, it should charger with no problem with the stock charger. If you soldered it up exactly in that stock rechargable pack then if there's an issue it's going to come down to one of two things. Either that little "charge" circuit found in a tiny side compartment (where the charger plugs into) is bad, or your Wall "charger" that plugs into it is bad. You could hook a volt meter up to the wall unit and see if it's putting out the proper voltage that it says on it.
Regardless of either problem, there's an easy solution...Buy the Accucel 6 charger and use that to charge your pack. Hook the charger up to the two battery terminals that make contact with the Sovereign via the alligator clips that come with the charger. Don't know which is positive or negative (can't remember...anybody?), then most volt meters will show a negative number if you hook it up the wrong way to the terminals to find out. The charger also has a reverse polarity function that will alert you if you hooked up to the wrong leads, but I'd be wary of trusting that unless you know the cells have some charger to them. I suspect if they are flat dead the charger wouldn't be able to tell if polarity is reversed and might try to charge it. What I did was check with a volt meter, and then marked the polarity on the pack with a magic marker for future reference. Reason why you need to charge that way and not through the little DC charging port is because that little circuit behind it isn't a direct pass thru to the cells and the Accucel won't work with that.