Turns out the fix was simple, and the problem due to my stupidity. My custom mail start/stop script called "make start" and the rc.d script, which meant the server was started twice. Once I'd changed this, and set an alternate pid file for the MSP queue in rc.conf everything worked perfectly. I had to change the ownership of /var/spool/clientmqueue to root:wheel (preserving default permissions of 770 worked). The rc.conf section for sendmail now looks as follows -
# Mail Services
## Core
mta_start_script="/etc/rc.sendmail"
sendmail_pidfile="/var/run/sendmail.pid"
sendmail_procname="/usr/sbin/sendmail"
sendmail_enable="YES"
sendmail_flags="-L sm-mta -bd -q30m"
sendmail_outbound_enable="YES"
sendmail_outbound_flags="-L sm-queue -q30m"
sendmail_msp_queue_enable="YES"
sendmail_msp_queue_flags="-L sm-msp-queue -Ac -q30m -OPidFile=/var/spool/clientmqueue/sm-client.pid"
sendmail_rebuild_aliases="YES"
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