I've just this second Automated the some parts in the Logic 5.5.1 Seqencer by twisting the Knobs you can only see this on the Virus channel/part which is set to Midi 1 in your logic 5.5.1 and you can only automate Cutoff and Resonance at this point in time,as far as i know.
I'm using OS 1.07..
you can automate other midi parts(1-16) in the Virus just select them within the VC and off you go again but All automation is only showed in the part with Midi 1 channel from the Virus,and it is like all automation within 5.5.1 just set the setting from Read to Touch within the settings for your Virus part within logic midi 1 of course...
Hope you know what i'm on about cause i've lost myself
