As the multithread test involves transferring lots of small files, I wonder if it is taking an unusual amount of time to establish the individual connections or if something is briefly pausing the start of each individual transfer. For example, some antivirus products scan the data at the start of each transfer to check for known infections and this sometimes causes a brief pause before allowing further data to download. I had issues with AVG in the past causing unusually long delays when downloading files.
If something is briefly delaying each connection, then this would likely cause the multi-threaded test to take longer as instead of a brief pause in a single transfer, there would be a brief pause in every individual transfer of the multi-threaded test, so with the 50 or so small files downloaded during the test, these pauses probably add-up more than any speed benefit of running batches of transfers simultaneously through the test.
If you can easily disable your antivirus product or firewall, I would suggest trying the multi-threaded test again with these disabled. The issue could also be within the ISP if they are doing something like deep-packet inspection on each connection that is established.