OK, I've looking into the HA Group scoring and what's happening is normal behavior. The threshold setting doesn't modify the HA score unless the members of the 'group' drop below the value, in which case that group' (of the trunk interfaces in your case) no longer contributes to the HA score at all. So, you'll need the active bonus to prevent failover if just one link fails.
You should carefully consider what scenarios you do want to cause a failover and calculate the weights and active bonus accordingly. See here for more information on how the scores are calculated: http://support.f5.com/kb/en-us/products/big-ip_ltm/manuals/product/viprion_configuration_guide_10_1/clustered_systems_redundant.html