Thanks again for your brain cells Rick.
That's what I had to do as ran out of time to solve it.
shift apple O dear
There seems to be something related to it involving text exported from Powerpoint, via INDesign and/or Iluustrator, that only effects After Efects.
So we stripped it all out with text edit but still seeing weirdness.
I just thought there may have been something noticed in the translation processes.
AICS5 to AECS6 say.
Like the Photo filter update in AE that you have to rebuild.
Or a weird thing I had where I had to add an extra frame if I was rendering a comp in CS6 (maybe a new 29.97 calculation) and remove it again in CS5.
It is one of those things you don't notice unless you are looking for it, unless you actually care about typography!
I am just pretending it is '98 and converting it all to Outlines.
At least it doesn't take a week to render anymore.