Is it normal for the Canon CR-180 to pause while feeding items?

Yes. The existence and duration of the pauses are related to the amount of processing required for each image.

The more powerful the PC, the less likely there will be pauses.
If you're using the USB interface on Windows 2000, installing Service Pack 4 may help improve throughout noticeably.

Speed Test Results using a Pentium 4 2 GHz PC with 1 GB of memory:

Black and White (binary): ~180 items/min

Grayscale (256 level gray): ~170 items/min