FINALLY! I think I found a solution! :D
The problem is that IE9 goes into Compatibility Mode because it interprets the code as quirky. If you enter F12 debugger and change to interpret as IE9 you'll see that it'll work.
The solution is to add this between your head tags:
<meta http-equiv="X-UA-Compatible" content="IE=9"/>
This will force IE to use IE9 standards. (The error was generated due to IE running in IE comp. mode and QlikView trying to set alpha layered background via the rgba()-function)
Can anyone confirm this?