Ephedrine HCL is a synthetic variety of ephedra that is manufactured in laboratories. Ephedrine is one of the alkaloids present in the herb ephedra.

The difference is mainly how its derived or manufactured. As far as potentcy, I am guessing its is much easier for the supplement/pharm companies to produce a consistent form of Ephedrine HCL with a common potentcy as compared to extracting ephedrine alkaloids for their products. This maybe why you feel the HCL more, but of course people react differently to different forms of stimulants.