Did some snooping around, it might be because of me not forcing the application to 32-bit mode.
Since flash is installed, it does try to load it, but as it's probably only installed for 32-bit IE it's failing when my app is running in 64-bit mode.
This is my theory at least.
I'll see to it the next version forces itself to run as 32-bit application.
(Basing this on:
http://forums.adobe.com/message/2126691#2126691)
Shame on Adobe though as this shouldn't really be my problem
