Hi all,
I 've seen some users having similar problems with other sequencers and I wonder if there is a solution to that yet.
Atomizer stops working soon after the project is loaded, sometimes straight after editing any MIDI or audio data in the sequencer - even slightest adjustment of one note in MIDI track can trigger this to happen for me. Although in Virus Control I can see that midi data comes through to my Virus TI Snow, but nothing really happens - input audio is just playing as if no data was sent. Sometimes some features still work, like gating / filtering with modulation wheel, but triggering loops with action keys does not.
Restarting Virus / Sequencer helps, but doing that every two minutes really sucks! 
For me the issue remains even after updating OS to 3.3.0.0 beta.
They say 'Atomizing loudly once a day keeps you happy :)', but I am yet to experience that