It seems to be selecting the files, but not visually showing me that in any way. It's basically impossible to use commander mode.
This has been tested on about 5 different PCs, but the same portable install on all of them.
When I grab a new portable version fresh without my settings file, the selecting works just fine.
This is a screenshot of me selecting the bottom 3 files in a FRESH portable version:
(I know the selection is faint but it's there...)
This is a screenshot of me selecting the bottom 3 files in MY portable version:
Note that immediately after taking the screenshot, my selection became visible. Hiding WinSCP behind something and revealing it again also reveals my selection.
Hopefully this helps. Let me know if I can provide any other info.