Maybe you used 12 cells but put them in parallel instead of series. I don't mean to sound insulting, but I believe that with the two battery packs, you hooked up positive to positve and negative to negative. When you hook up 2 batteries to make a "12 cell pack", you're supposed to hook up the negative from one to the positive of the other so all the cells are end to end.
I agree with Serum and Lipomaxx. The 12 cells were probably wired in parallel, so the only speed you gained is from the extra current capability of the dual packs. The batteries are a huge limiting factor as well. One good 7 or 8 cell pack will propel that thing to the mid 40s pretty easily. The Kokam Lipos are awesome as well, and would really turn it into a rocketship.
Get get 1 3s lipo and then save your money, and get another one. A 3s3200 will go about 42 mph with 18/86 gearing. The 2s won't be any faster than 6 cell NiMH.
I bet the 2s LiPo would be faster than the 6 nimh cells he is currently using! you could even get two 2s LiPo packs and run them in parallel (6400 Mah) and be about the same weight as 6 nimh cells. Personally, I run the 3s pack or above, but I run bigger trucks!