How many trials do you have per condition? With a small number of trials in the deviant condition, and a small number of participants, these things can happen. 

The ISI would not cause this per se, however, have you considered looking at effects of the previous trial? You can analyze the baseline intervals as a function of what type the previous trial was, and see if there is a difference in the period following deviants or standards.

You could also try to randomly sample as many standard trials as you have deviants per participant, and then re-do your analysis and see what happens. You can make a loop and do this many times, and then look at the median p-value.

All that being said, even if you have a baseline difference, it might not really matter: *this is what baseline correction is for*. But I agree that it's disconcerting.

I'm also a bit confused why you would use an ANOVA to compare two conditions, and not a t-test. Maybe I'm not understanding you design completely.