There was just a post about
this last week, I believe. Once I started Remicade, mine started coming back atypical for the first time in my life and they were atypical every year that I was on Remicade. My HPV tests came back negative. I switched to another biological and this year, it came back normal. But yes, someone posted a link to an article in a medical journal sometime in the last year or so saying that women on immunosuppresents or biologicals (don't remember for sure which one but it may be immunosuppresents, since I know you said you're not on a biological) were more likely to have atypical paps.
Crohn's Disease, Acid Reflux/Gastritis, Hashimoto's Thyroiditis, Endometriosis, Arthritis, Depression/Anxiety. Too many meds to list them all. =)