From my experience I'd say that if the pipe was sealed and jetted correctly, but still made less power than the blowing pipe then there's a chance that the tail pipe may be too small a diameter (or too long) for your tune. A small diameter tail pipe will give good power, but only on very short bursts (drag racer for example), due to the heat build. A larger diameter tail pipe actually reduces power (usually) but allows this slightly lower peak to continue without over heating and the enevitable power loss. The difference may only be 1mm, but it will make a big difference in the way power continues to be made as things heat up.

You say you think the chamber is too small. What part do you think is too small? The shape of a pipe depends on many things, porting being just one of them. A big bellied pipe can over scavenge if the the porting is not designed for this type pipe, or a small bellied pipe can leave a gp style cylinder gasping in the midrange if it doesn't pull hard enough in the first stages.

Clean and seal up the pipe, jet it properly and see what happens. Can't make any judgements if things aren't running properly.