The 1400 has a slower bus then the 6300 and, depending on the model of CPU you have, also has L2 cache which can make a big difference.

I know that the 1400 is the last Nubus based logic board Apple made. Perhaps that has something to do with it as well.

It could also be an indication to find another hard drive. I found the original drives to be slow and installing even a newer 2GB model or better can significantly improve performance.