You say 90 days is the standard turnaround for mss, but what about for mss from existing clients?
Before signing with my current agent, he read my first manuscript virtually overnight (knowing he had competition from another agency). It's a year later, the novel hasn't sold, and now I've delivered another ms, and there's been no word for a month. Should I feel neglected or not?
Miss Snark must shamefacedly admit she has one or two manuscripts lying around here with cobwebs that are from clients. Yes of course you should feel neglected but the real question is: should you do anything irrevocable about it like depart from the agency, hurl invectives, or threaten your agent with the arrival of serial scrubbers? Answer: no.
Things get backed up here like plumbing at a family reunion, and it's just about as pretty. I'll come into the office on Monday with a clean desk, a cheerful countenance and next thing you know, my hair is on fire with things that need My! Immediate! Attention!. Those things do tend to get my attention and by the end of the day, or week, it's all I can do to crawl home and gaze longingly at Mr Clooney on DVD. All my good intentions to read a manuscript have fallen by the wayside.
Your course of action is 1. make sure s/he has the thing. You'd be surprised how often things aren't here that the post office says should be. I suspect Miss Rumplestiltskin, the retired librarian in 3X is responsible for this.
2. If indeed it is there, drop the agent a note that says "what's your time line". Then double it. Then if you haven't' heard a peep, then you start thinking about what major steps to take.
The key is to ask the agent what his/her timeline is. You don't impose yours but you do ask him/her to adhere to theirs.