There might be a few reasons for this, most obvious is if you are confusing Win32 and x64 versions of the applications. Provided that there is no confusion, note that some filters are blacklisting themselves to be not available in specific applications/processes. For example, MainConcept might want to enable their filters for GraphEdit as a demo mode for developers, so that they could make sure the filters are good and pay for commercial version where filters are also available for applications.
In general, when there is no special intention to selectively disable filters for specific applications, fitlers are equally available to all applications using DirectShow API.