I couldn't find a bug tracker for ClearOS, and sales haven't responded to our email about transitioning to ClearOS, so I'll just post it here.
The protocol filter seems to work as expected with most protocols, but some don't seem to show up in iptables. Two examples are Counterstrike and Day of Defeat.
Another bug is in the Layer7Filter.class.php API file. The regular expression it uses in GetStatus doesn't match correctly when the number of packages or bytes gets "K", "M", "G", etc. appended. This causes the Protocol Filter Report page to show zeros in those fields after 99,999 blocked packages or bytes, when iptables begins to report it as "100K".
Hope this helps someone somehow