My opinion is that the probiotics will definitely NOT hurt anything, so go ahead and take them anyway. I guess I'd take them halfway between doses of your antibiotic to give them a small chance of surviving.
Status: Remission since late May 2009!
Symptoms began in November 2008, ~4 weeks after giving birth to my son.
Diagnosed with pancolitis on 1/30/09
Currently taking Asacol (400mg 4 pills 3x daily), Rowasa twice weekly, Natural Factors Ultimate probiotic 12/12 Formula, and Zoloft (25 mg).