After upadting the mark5B software (following the instructions found at http://www.haystack.mit.edu/tech/vlbi/mark5/downloads/Mark5BUpdate.pdf) problems were still seen using scan_check on the 6 TB SATA drives. To correct this, I ipgraded the Mark5B firmware from 12.41 to 15.30, following Dan Smythe's instructions. Several environment variables had to be set and have been included in oper's .bashrc file.
export STREAMSTOR_BIB_PATH=/usr/local/src/streamstor/linux/bib
export SS=/usr/local/streamstor/linux
export PATH=$PATH:/usr/local/bin/streamstor/
Once these were set, the flash_upgrade was carried out by
cd /usr/local/src/streamstor/linux/lib/gcc_v3/util/
./flash_upgrade
This will need to be done for each of the mark5B recorders.