One problem with fantastico is, that they don't update regularily. I am surprised that you already got 1.9 with them and not something like 1.87 or even 1.81. But it is a long time ago that I last had a look at Fantastico.
In 1.9x there is an easy update function. But it seems that the fantastico version doesn't allow you to update, which might be caused by modifications that they made to include it within their tool.
I have given up to use fantastico, because usually the installation of the included tools is quite straight forward. Might take a few minutes more, but saves you headaches in the future.
Problem is also, as the developers don't know how fantastico is implementing Limesurvey, it is difficult to help.
If Limesurvey had a general problem with the IEs the forum would be full of complaints, so we have to see what is wrong with your particular installation.
Not being able to add answers to multipe choice questions sounds like a problem with Jquery. What happens when you use the quick add feature instead of the "+" sign?