I have performed research and the I have come up with the following: Your cat may have an underlying Herpes eye infection.
Herpes-virus is extremely common in cats and is similar to the human herpes simplex virus which causes cold sores. Once a kitten is exposed to the herpes virus it becomes a permanent inhabitant of the body and only causes active infection when the body is stressed or immunocompromised.
Giving multiple vaccines simultaneously can cause stress to the immune system (in the susceptible patient), thus allowing the latent herpes virus to become active, and in your cats case, cause a herpes iritis (infection and/or inflammation of the iris). Once the patients immune system has dealt with the vaccine invasion, the iritis resolves. The inflammation of the iris from the herpes virus can cause an eye color change.
This is of course just speculation, and is purely theoretical. I will continue to post answers to this question as they come up.
This is truly unique!
I will have to post your question on VIN (veterinary information network) to the veterinary ophthalmology department. It may require a few days but as soon as I get an answer I will post it here.
Incidentally, in our practice we give a maximum of two vaccines per visit to avoid vaccinosis complications. After the first year we perform vaccine titers on all our patients rather than give them unnecessary vaccines.