My group plays it that Invisibility is invisiblity, no matter how much flour, fog, rain, water, or what have you is thrown about. My personal take is less restrictive. I'm all for letting player creativity help out in pinpointing the invisible creature's hex (footprints in the sand or flour, the vague outline of a person displacing fog or rain, the splashing of invisible feet in shallow water), but retaining the 50% miss chance.
Using unconventional methods to suss out the invisible person isn't really covered in terms of hard numbers, its one of those things that GMs have to adjudicate on the fly (does covering the floor in flour not help in locating an invisible person, locate them immediately, or give a bonus of some sort to the spot check?) and so there's going to be some variations there.