I don't know if this is any help to others, but I just went through the update process again so it made me remember this...but I leave mine in Auto and find that things will often work on the first plug in a search for a open comm, but then I try a second time and it will not...so I unplug the USB plug, and plug it in again and then it finds one.
This last try was on my Laptop which I point out because there shouldn't be this much comms, but yet first it found Comm 22 was available, so I updated the TIU with that, then I tried my first handheld right after and it say it could not open Comm 22, so unplugged the USB and re-plugged and then for the next try it found Comm 23 was open, so I updated it on that. Went to do my second handheld and then it could not open Comm 23 so I unplugged the USB out and in again and then it found Comm 22 was open.
Also sometimes it can help to try a different USB in plug on the Laptop as well.
I have had this Laptop for probably 5 years but at the time I bought it, it was a $1,500 Dell...so its not crap, as well it runs everything else I have ever plugged into it fine and without this issue.
Basically if I had to guess I would say the MTH loader has issues which being that its free its understandable, but all in all and as it was first built to work with a older fixed port type system, does not seem to have been brought over to the find a port through the OS type current system very well, so you just have to mess with it till things finally work out.
Hope that is of some help.