Hmmm, thats a tricky one...
My DD was sleeping through for a few weeks when we started solids but stopped coincidentally with her 6 month immunisation. She wakes any-where from 2-3 times a night, not matter what we try.
Our CHN said that it is quite common for girls of her age to start playing up. It could be any-thing from growth spurts, hunger, teething, comfort, separation anxiety (etc). She also said that these little ones can be rather manipulative - testing boundaries etc.
I would think if your bub is other wise happy, no temperature (etc) then I wouldn't think there is any serious reaction to the immunisation. DD is usually a bit cranky for a few days after hers.
My DD changes her patterns quite regularly as does most of the 12 bubs in our play group. Its pretty tough on poor old mum and dad though when you have been use to getting decent sleep.
As for the flat head a little tip that might work for you is putting a mirror / toy on the side of bubs cot. I use to switch sides as DD loved staring at it and always fell asleep looking at it. Once she started playing with it too much I took it out and she naturally moves her head throughout the night.
Other than being very jelous that your bub slept through from 6 weeks (LOL) - I wish you the best of luck. I am sure there will be lots of good advice from the great mums out there that will help.
DD is 3yr 8 months - DS is 6 months