Hi Face-man,
I don't think it's the same problem.
The OP is having problems opening single files (word and Excel), which have to be downloaded to a PC so that they can open. When they click on these files in FireFox, they get a dialog box that asks them if they want to save the file.
This setting isn't enabled in IE so the browser tries to open the file but other security settings kick in and close the file.
The symptoms of this are similar to a blocked pop-up.
If this was a problem with an outdated backend then I guess that they would have a the same problem when using FireFox?