Processing Submissions on arXiv
My guess is that the time in processing status follows a roughly bimodal distribution. The first peak is when everything goes well, and certainly occurs before even a day has passed. The second, presumably broader, peak depends on how long it takes the automatic processing system to fail, and someone to have a look at it. I don't know where this second peak is located, but the point is that I expect there to be two "normals", depending on whether your submission had technical issues or not. Personally, I'd feel justified in contacting arXiv after three days or so.