Your biggest partition is 6MB? Your CF card is 8MB capacity? Are you sure you're not getting your GB and MB mixed up? I'll assume it's an 8GB CF card and that your largest partition is 6GB. I'd first run the Check4GB tool so you can see at a glance any current issues:
http://thomas-rapp.homepage.t-online.de/download.htmlLet us know if it detects any problems.
Your boot partition should be within the first 4GB of your drive. Check you are running PFS-AIO on both partitions. Check the DOSTYPE and MAXTRANSFER are correct on both partitions.