Freescan works perfectly fine for what you want to do as does proscan and he mentioned about SET for the autoscan for the port. The others more-less disregard previous comments TBH.
What you have to do is this each time, same with any other software is to have the software find the correct COM port is all.
This is what I use,
Cable for 996XT
In Freescan, assuming you want to program(Upload) to the scanner,
Click on "Scanner", Upload programming
click the box where it shows COM, its between the Auto and Start Upload boxes.
Then after clicking COM box,
click on "Start Auto" box, it will then find the scanner.
Then press Close and do what you need as Freescan has found the correct COM port/baud rates.
I usually will have in the communications box have these ticked-
Replace any....
Send custom...
Dont send...
Send system...
Automatically...
Once you have everything the way you want in freescan, I also tick the "All" button and the Erase....
Same procedure to Control Scanner or Download - that is copy the scanner info into Freescan.
The videos can help, although they didnt show about finding the COM ports and had already setup communications.
FreeScan User Guide - The RadioReference Wiki
If it still wont connect, IMHO its a driver issue or the cable.