Two separate issues can be the source of the problem:
- SBS Monitoring database is too large and is using large amounts of disk space. If so, check this out: http://blog.korteksolutions.com/the-sbsmonitoring-database-is-nearing-maximum-size-on-sbs-2008/. I used the downloadable new database from this location and it worked great.
- Missing indexes in SBS Monitoring database cause high disk and maybe processor activity. If so, check this out: http://social.technet.microsoft.com/Forums/en/smallbusinessserver/thread/d195baac-da8b-4387-9079-c55d5e1879b4