Well, as I see it, bw.conf will throttle bandwidth to the SEPM, irrespective of GUPs or clients. Both GUPs and clients fetch content from SEPM through port 8014 (default), which is handled by Apache.
So the bandwidth value in bw.conf is the maximum reasonable value you can enter in the GUP configuration form.
If bw.conf is on 100 Kbytes/s, you need to multiply that by 8 (8 bits are 1 byte), so enter 800 kbps (kilobits per second) in the GUP form to max the bw.conf bandwidth.
It's perfectly understandable that the IE download is faster. It is only throttled by the bw.conf setting, but the GUP has to respect the lower value in the GUP form.