That's what I do, I alternate. Chris Colby mentioned it in a basic brewing podcast last year, (the one on fermenting in kegs.) I also sometimes don't use the same sanitizer I used on brew day on bottling day a month later. So batch A may be starsan/iodophor but batch B may be iodophor/starsan, maybe then batch c is starsan/starsan, and d would be iodophor/iodophor.
It's called a house germ...and it develops over time...
On Craftbrewer radio they said it usually happens around the 10th, the 30th and the 50th batch...even the pro's deal with it (the Brewer at New Glarus said in an interview that a commercial brewery operation gets a 3 year grace period before their first infection)
I got an infection around the 20th batch, I replaced my autosiphon, bottling wand and all my hoses and temporaly change my sanitizer, in case the house germ was getting used to it...
They talk about the "timeframe" of infections, and how it is less likely for a first batch to be infected...it tends to occur around the 10th batch and the 50th...When the equipment gets more used up, and "house germs" start to build up. They used the term "house mouth" in the discussion, how we may not even notice, because we're sort of used to the taste of our beers, it's usually NOT a regular drinker of our beers that notices it.