-square doesn’t actually set the texture to be POT as well, there’s now a separate -pot function which does this. So for your command line, you’ll need to use:
FYI, it’s worth noting that in the old version of the command line, -square did in fact make the texture power of two as well. So I guess that’s what you were thinking of?
-flip y,flag didn’t work in the initial release of the new command line, but it should work in the most recent versions. If you find this to not be the case let me know.
If you have any other problems with the command line please don’t hesitate to ask!