I believe the speed control will still work without a capacitor unless there is a short.
I may be wrong here..but I'm pretty sure the power capacitor is really there to help protect the speed control from damage and keep it running cooler. If the issue is with both speed controllers, I highly doubt the capacitors are your problem.
Are you running NiMHs or LiPos? If you are running NiMHs, do you maybe have the LiPo cutoff set by chance?
I never had this issue when I was running a Sphere Comp (then again, mine has been in waiting to be warrantied for 5 of the 7 weeks I have owned it.) I was switching back and forth between brushed/brushless running NiMH cells no problem.