You may have a bad SD card, try a new one (they're cheap anyway).
The MD5 sums are generally computed after the backup has been done (assuming everything went fine).
I.e. the process up to CWM 5.x is (CWM 6.x is different due to dedupcication):
- CWM generates a backup and stores it
- Then md5sums of all of the above files are computed
- The md5sums are also stored in a single file
The hard work is all done in (1), steps 2/3 are just a single md5sum computation per file and a final store of those in another file.
If the MD5sums mismatch the backup files there must be a problem with your storage eventually (most probably). What is also possible: Don't rip out the battery and reboot, use CWM's reboot option (files may have not been written do disk fully yet).