I did a little more testing.
In my setup I have Media Center and Media Server start with Windows. I also use the "Minimise to system tray" option. I'm currently running MC25.0.98 on my HTPC, which is the only system I have an IR receiver installed in.
After rebooting my HTPC so that testing started "clean", I filled Playing Now with tracks and then minimised MC to the system tray. Play didn't do anything.
I started playback in MC Standard View and then minimised MC again. Pause didn't do anything.
I tried the above with MC maximised but with Chrome in focus. Didn't work.
What did work was Stop, Skip Forward, Skip Back, and the Green Button (or in terms of MCE commands on the Harmony, Media Center), which opens MC to the TV Guide. Some of the other standard MCE Buttons/functions such as Live TV worked as well. I tested with both my Harmony set up as an MCE extended command set remote and with a separate standard MCE remote. Both worked the same.
So I have to say that IR Commands are very spotty when MC is minimised, or not in focus.
In testing, when pressing remote buttons multiple times, I managed to make MC unresponsive altogether. i.e. After selecting Live TV I tried to stop playback, but could not. None of the remote Stop, OSD Stop, menu Stop, etc. would work. Live TV wasn't actually playing, but MC said it was. I had to reboot the HTPC twice to get it back to a working condition.
IR Commands did used to work when the Media Server was running. A search of the forum will find lots of such discussions.
I think IR Commands in MC are broken. Well, I actually think IR Commands in MC have always been broken, except for the basic commands. But something extra seems broken now. I don't remember any fixes ever being applied to Remote Control capability in MC, except perhaps for the IR Blaster setup, which on my system won't learn anything at all. But I don't have a Blaster plugged in, so that could be why.
PS:
Note that you have left a "0" off the MCC command. It should be MCC 10000 for Play/Pause. Also, you don't need to add the full path to the mc25.exe program. There are copies of the program in the "C:\Windows\System23" and "C:\Windows\SysWOW64" directories, so Windows will find and execute the command without the full path. But let me just test something else...
PPS:
Okay, I have a solution for you. I don't like it. Or more correctly, I don't like what MC is doing.
I picked a Remote Control button that I know MC sees, being the "DVD Menu" button. I reprogrammed it to send the /MCC 10000 command. That didn't work. In fact, MC still acted as though I had pressed the "DVD Menu" button, as though I had not reprogrammed the button at all. This is what you noted previously.
Given that MC appeared to be responding to default MCE IR Codes with default MCE commands, even though the associated command should have changed, I decided to learn the "DVD Menu" IR Code against the "DVD Menu" option in MC settings. With that done MC responded by Playing/Pausing tracks in Playing Now, whether MC was in focus or not.
So I went back and learned the IR Code for Play/Pause using the Play button on the remote. MC then responded to the Play button on the remote by Playing/Pausing tracks in Playing Now, whether MC was in focus or not.
Note that when you learn an IR Code against a standard MCE command, MC will warn you that you may end up with duplicates. Ignore the message and go ahead anyway. However, watch out for duplicate commands being sent to your PC. i.e. The standard MCE command that seems to be built into MC, and the command programmed through options. It is possible one button press could send two commands, but I haven't checked that. I have seen problems with learning standard MCE commands that MC already knows about in the past though.
So for your situation, probably all that you need to do is learn the commands that you want to work when MC is not in focus, and they should work. This is against the advice I have received, and which I repeated above. I think the IR Commands functionality in MC is broken. But this workaround seems to work.
Good luck.