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@gary,
If you distibute calibre in binary form you must also distribute it in source form to anyone receiving the binary version. This includes any modifications you have made to it.
If you use source code from calibre in another application you must license the program in a way that is compatible with the GPL v3.
If you use calibre as the basis for another application and calibre is a substantial portion of the other application then the GPL requirements apply and your application would be considered a derivative work. If you can say no to these questions your application is not considered derivative. Do you use any source code from calibre? Are you distributing calibre? Most important, does your application require calibre to work?
From what you described it sounds like you are fine. As long as calibre is a small part of the functionality of the application. The user installs calibre there self and your application will use it if available. The application calls calibre using system calls not linking to it. Also if your application is structured in a way that you can use multiple different conversion programs you are fine. Your best bet is to do what you're doing and keep calibre separate and working at arms length from your application. User installed and not linking will keep you in compliance.
In the case of the ebay listing, if the person includes calibre's source code on the dvd then they're fine as far as calibre is concerned.
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