I'm not sure what the answer is, but;
Win+1 on Windows is a predefined key combination, and opens program that is represented by the first icon on the task bar. So do you mean that you have the MC icon placed as the first icon on the task bar, and hence the Harmony and keyboard combination are just using the Windows capability to launch an application, or have you tried to program that Win+1 combination into the MC Remote Control commands?
If using the Windows capability, check that the icon is still first on the task bar and still has the correct settings after the update. Or perhaps removed that icon, then add it back using the icon under the Windows Start menu.
Regardless of above, if you are getting a pop up from the icon on the task bar which shows the Rewind, Play, Stop, and Fast Forward button, plus a red X in the corner when you hover your mouse over the pop up, then the MC Client is running and is probably just minimised. If you can't get to it via Alt-tab, clicking on the MC icon in the System Tray, or right clicking on the icon on the Task Bar and selecting JRiver Media Center 21, or simply clicking on that icon, then something is screwy in Windows.
You don't say whether you have rebooted the PC after doing the update, or when this problem happens. I would try that first thing in this case, as it seems it could be a Windows problem. I've seen similar with other programs before. Also, you didn't update a video driver recently did you? I seen that precipitate the problem, requiring one or more reboots to fix.
The "Media Center 21.exe *32" process is the MC Media Server process, run in the background to record scheduled TV, run background processes, and service MC Clients. Killing that process will kill the Media Server and the MC Client running on your PC.
Also, do you have MC set to "Minimise to System Tray" under Tools/Options/General/Interface ? If not, turn that on and see if you get an icon in the System Tray, indicating that the MC Client is indeed running. Note that if you just close MC, and then immediately try to reopen it, MC may not open, as it can take about 30 seconds for MC to stop all processes and fully close. If that is what is happening, close MC, wait 30 seconds, then reopen.