Where to start? There are a lot of issues raised in your posts so far BoomBoom.
First, JRiver Media Center isn't a copy of Windows Media Center. So naturally things are going to work a little differently in MC (JRiver). There will be a learning curve. It isn't that MC is worse than WMC, just different. WMC certainly wasn't perfect. But you got used to it. I'm sure you will get to love MC as well.
One of the reasons that WMC was so painless to set up is that it is a Microsoft product, and therefore every software, hardware and service developer tested their products against WMC. If their products didn't work with WMC, they weren't going to be successful. As a consequence, Microsoft could make a bunch of assumptions about how people were going to want to use WMC, and just set it up the way they wanted. For example, Microsoft influenced EPG data providers to a massive extent, and then provided the EPG data free to WMC users. Therefore, it worked, at least for users in America and a few other select locations around the world.
Also, being free software, they didn't have to try to meet user's requirements. They just built it and delivered it, and expected people to use it as it was. In the early days there were many many problems with WMC, and lots of third party forums and web sites sprang up to help people make it work for them. As a mature product WMC was much easier to use than the earlier versions. Hence, it was painless to set up.
MC can replace WMC in all areas except encrypted Cable TV recording and playback. That issue is being addressed now.
Take note of Jim's comment about WMC interfering with TV in MC. They can fight over TV tuners if both are active, even if WMC is not actually running, because it runs two services in the background to enable TV recording a playback. Disable WMC and both WMC services before testing MC TV capability.
Next, MC understands MCE remote commands by default. You don't need to program it, or teach it any Infrared commands to make it work. If you want to control other devices outside your PC using IR, then you do need to teach the IR Blaster in MC, so that it can blast commands to the external devices. But if you aren't trying to do that, and you shouldn't until you learn how MC TV works, and get it working properly, then you should not have made any changes to IR commands in MC.
If you have made changes, go to Tools/Options/Remote Control/Devices & Options, then in the box "Selected input devices" make sure that "Microsoft MCE" and "Remote, keyboard, gamepad, or other HiD" are selected. If you have such a device, then they should be marked as (Active). So if MC sees your MCE IR receiver in your PC, "Microsoft MCE" will have the suffix (Active).
Now click "Back' and select the "Commands" link, then click the "Restore Default List" button to restore default MCE IR commands. In the column "Learned Trigger Code" all commands should have a "?" next to them. This is normal, and correct when using a standard MCE remote. You can learn about customising commands later.
That should be enough for now. Before you ask more questions, I encourage you to read some of the threads in the forum that other WMC users and JRiver personnel have posted. For example;
http://yabb.jriver.com/interact/index.php?topic=100685.0http://yabb.jriver.com/interact/index.php?topic=100399.0http://yabb.jriver.com/interact/index.php?topic=98239.0http://yabb.jriver.com/interact/index.php?topic=79837.0Note that quite a few issues raised in those posts have been, or are being addressed now. The developers have made huge improvements in TV functionality over recent months, and continue to improve it.