"Inputted" may be acceptable per Oxford, but it sets my teeth on edge; my ear wants "input" to follow the same rules as "put". I suspect I'm not the only one, which is probably why you're being forced to change it.
EDIT: This question/answer has been getting a bit of attention recently, so I'd like to clarify my comment below. There is a verb, putt, meaning "try to hit a golf ball into a hole by striking it gently so that it rolls across the green", which is often confused with put "to move or place". (The confusion is natural, since the golfing term comes from a Scots variant of "put" - but the two words are distinct, and pronounced differently.)
The past tense of put is put; the past tense of putt is putted. Since input is formed from "put" rather than "putt", it seems logical that its past tense should be input, rather than "inputted"; "inputted" sounds like a demented golfing term.