That's an interesting point- I think that would depend on what individual is focusing on, and whether your random animations/events would some how be overlapping with what is being chosen.
So for an example- say you have your action selection icons (power/weapons/etc.), and those go from one color to another with high contrast. Great- that will elicit the P300 response. Now, if you have totally separate events occurring which float over those items it could be distracting and lower the accuracy of the P300 as they are now focusing on something which you aren't trying to have them target.
However, if your animations/events are happening around their peripheral that shouldn't affect the scenario- as that is exactly what the oddball paradigm does normally! Does that make sense?