i myself have now ran into this issue. and it don't matter if i put putty C:\Putty\putty.exe or %PROGRAMFILES%\PuTTY\putty.exe. it honestly does not matter where i put it. same stupid error over and over, and yet just this morning i was in WinSCP and Putty and killing my bopm and restarting it just fine and dandy, and now all of a sudden its "internal error invalid port number" over and over - and i have tried a lot of things i found about this issue all over the internet.
who knows maybe someone out there MIGHT have a solution to this issue.
Running Windows 7 in case anyone wonders about the OS.