So it sounds like what you're describing is that the multichannel film soundtracks aren't getting downmixed correctly (you're missing the center and the subwoofer in your downmix). If I read your description correctly you have a stereo 3-way system? If that's the case, you need to open DSP Studio and go to the output format tab, and look at your "channels" settings. If you have the channel count set to "5.1," that's not the correct setting: JRiver doesn't know that you need it to downmix to stereo and is just passing through higher channel count audio so you're losing that information when you run your convolver later in the chain.
The correct settings (assuming I've understood your setup) should be: set the channels to "2 channels (stereo) and then set "extra channels" to "4". Also make sure that you have "JRSS mixing" selected under mixing (the alternative setting "no upmixing or downmixing" is wrong for your use case because the center and sub won't get downmixed with that setting).
Those settings (2 channels; 4 extra channels; and JRSS mixing enabled) will give you six total channels for mixing while ensuring that surround videos get downmixed to stereo first. If you try that and it doesn't solve your problem, post back with more info about your DSP studio settings.
The "tempo and pitch" probably isn't your problem, that's a thing that happens when you enable video clock; it's usually harmless.
