It sounds like the update from the really old version of Mach4 somehow futzed your configuration. Do you (hopefully) have a copy of your profile directory from before the update? And do you remember what (6 year old) version of Mach4 you were running? If you have your old profile (specifically the "Machine.ini" file) and your new, revised, not working profile, I may be able to help get the settings from the old one into the new one.
Or you can do this yourself. Re-install the old Mach4 version IN A DIFFERENT DIRECTORY (i.e. not C:\Mach4Hobby) and put your old profile in the "Profiles" directory. Run the Mach4GUI.exe from the directory in which you installed the old version. Take a screen capture or write down all the settings from your motor tuning, axis mapping, inputs and outputs and spindle tabs.
Then run the current version of Mach4 and change the configuration to match what was shown in your old Mach4 version.
PMDX keeps a repository of old Mach4 releases in case you don't still have the installer for your old version. You can find them here:
http://www.pmdx.com/Downloads_Mach4/Mach4_Hobby_Releases/Now that I look at the old releases, if your previous Mach4 was 6 years old, that means it was a Mach4 version 1 release. I seem to recall that things changed pretty significantly between version 1 and version 2 Mach4 releases. That may be the issue, and the newer Mach4 versions can no longer convert the old INI files.
One more note: When/if you re-install the older version of Mach4, it may change your desktop icons to point to that older version. To get the icons back to pointing to your new Mach4 install you may need to re-install the new Mach4 version (it is OK to install it on top of the existing install, as long as you aren't using "Mach4Mill" as your profile).