I am working on QlikView 9 SR3 server & IE Plugin.
Using IE plugin, If I make the FIRST CLICK of the qlikview application on a button, It does not execute that button. Then if I click the button again , it works as expected.
For me it happens only once for every application opened in the access point. It is like just ignoring the first click made on the application.
I remember a client with this problem during the early releases of version 9. I don't remember seeing the problem again and can't replicate the problem on a version 10 SR1 server, so I would try updating the to a newer Service Release. To be sure you might want to review the release notes of each SR to see if the bug is mentioned as fixed.