I have had this same issue in the past. Rough idle when engine is warm for about 30 seconds. If I let it sit it will smooth out. If I try to drive right after warm start it will every once in a while throw a misfire cel. I am sure it has to with cranking or startup tables. On the plus side with my modified cranking tables I have been able to one crank start my car on 100% E85 at 20 degrees.