I'm on Apriso (mesalamine oral) and mesalamine enemas, and haven't noticed any problems. But, I'm on the pill as well!
My guess is that your period is wonky because you're in such a bad flare. When your body weight drops suddenly and/or you're very ill, your body kind of goes into preservation mode, which can affect your periods. A lof of women with very low body fat rarely have periods.
Status: Remission since May 2009!
Symptoms began in November 2008, ~4 weeks after giving birth to my son.
Diagnosed with pancolitis on 1/30/09
Currently meds: Apriso (4 0.375g pills ONCE!! daily), mesalamine enema twice weekly, Natural Factors Ultimate probiotic 12/12 Formula, and Zoloft (currently tapering; 12.5 mg).