Hi Ken,
Adagio specification files (including checks) must have a file extension that matches the data. If the 2nd company has a different file extension, then you need to edit the extension on the copied spec file to match.
Whenever you access a spec file finder (either in Edit Banks or Print Checks), the program looks for all appropriate spec files with the same extension and builds the list.
BTW: Don't worry about the file type description of 'Windows Installer patch'. All this means is that your machine has associated files with that particular extension to an application, in case you simply double-clicked on the file. The fact that it's different than the others certainly indicate that you need to edit the spec's extension to match.