Confirmed, it will be fixed in the next release.
Thanks for your thorough reply.
Meanwhile, may you need a workaround you can reference your putty.exe directly into the catalog using the Apps package via the extra_paths setting, simply by appending C:\KiTTY\PUTTY.EXE to it. Be careful though to use the item created by the Apps package then, instead of the one created by the PuTTY package, by watching the status bar once you have selected the item (i.e. should be written: Apps item).