One of our users is having a recurring problem with a virus. It has happened to this user on two different machines, in each instance infecting the same program with the same virus. 

Malware bytes detects the malware, and yesterday I cleaned the system. Note that MSE doesn't find anything. Malware bytes real-time scanner is running too, but I checked again today and the system is re-infected. 

It's a Win 7 Pro SP1 system, it has the latest updates, it's running Windows firewall (as well as being behind a corporate firewall), MSE and MBAM on the system, and still it gets re-infected! 

I've scanned the user's network drives in case they're picking it up from there, but so far nothing's been found.

How can I get to the bottom of this recurring virus problem and stop the system from getting infected once and for all?