lumpasmelly poor you that's hardly helpful for your peace of mind...! If it's any comfort it sounds to me like speculation on her part, erring on the side of extreme caution.
There is no evidence at all that a vaccine would damage the baby's development.
The reason they don't advise it in the first trimester is that is when all the organs and systems are forming and it's a fragile process and nobody knows comprehensively which delicate balances of the mother's body chemicals can affect it or make it go awry.
Also because in the first trimester the risk of a miscarriage is highest anyway, so the statistical probability is that some women vaccinated in the first trimester would go on to have miscarriages anyway and although it most likely would not be linked to the vaccine, nobody would ever really know and you would always wonder, as many people do, whether they did anything that caused it.
After 13 weeks almost everything physical is fully formed, amazingly, and just has to mature, grow and develop.
I can see why she advises waiting until later towards the third trimester. But we can't choose if or when we catch a virus (if we ever do, chance is also big that you escape it altogether!) and it seems the immunisation experts believe that the chance of swine flu harming the baby, if a mother caught it, is higher than chance of the vaccine harming the baby.
Sounds like you need a bit more time to think about it anyway.
Blimey in one way I'm glad I've already had the jab as there's nothing I can do to change it now.