Triggles, ds1 does this and it comes back every single time he is going into emotional freefall.
We also thought there must be something wrong with his eyes and got him an eye exam, but it was all clear. At it's worst he became very distressed as it stopped him from being able to read and reading is/was his escape in times of stress.
We went through a time, when he was at his worst anxiety-wise of thinking he was going to end up with a Tourettes dx as well as ASD. He was blinking, eye scrunching, throat clearing, vocalising, had a head/neck movement thing and also developed some hand-movement type tics.
Each one diminished as his stress and anxiety levels came down and he was better supported at school. Now if we see them starting to creep back in we know it's time to do some investigating and track back to the source of the anxiety or stress.
He is currently stressed and anxious about school year transition and his hand movement/s, throat clearing and head/neck movements are all resurfacing. We are trying everything we can to support him through his anxiety and the eye one hasn't come back yet. If it does, we know things are really bad. I know from experience that they will ease off a little by mid summer holiday and then get much worse before he goes back in September, accompanied by terrible upset stomachs, migraines and reflux.
I have a feeling we will be seeing them a lot over the next 12 months, as he is already really anxious about going to secondary in September 2013.