Two interesting things I had read a few days ago. One, apparently MS claims that MSE doesnt skip files like other vendors to reduce scan time. That would mean that compressed files such as .rar and .cab files would be loaded into memory and scanned each time MSE is run, that would naturally slow down the process. So MSE may not be flagging files as safe and probably scans them every time.
The other is that full scans or at least scheduled scans are subject to 50% CPU throttling.
See these 2 threads. Slow "full scan" on MSE 2.0.657.0 Full scan took over 10 hours!