I have been using WMC Remote (A9O-00007) on a PC that is connected to my TV. I like this remote because it also controls the TV power and volume. Two days ago the computer functionality of the remote stopped working, but the buttons still light up as well as the light on the receiver. It also still works to control the TV. There has been no change to my computer software, no updates, etc. It was working in the morning and not working that afternoon. In between those times it had fallen between couch cushions and my only guess is that multiple buttons could have been pressed for an extended period of time. I have tried replacing the batteries and also tried the remote on two other computers in the house. Nothing works. Has anyone else had this problem and know how to fix it?

I understand that your Windows Media Center Remote does not work on your computer but works with the TV. You might experience this issue most likely if the necessary drivers are corrupted or missing.
In order to help you better please provide us the following information:
What is the make and model of your computer?
Method 1: SFC scan
Run SFC scan on your computer and check if it helps.
Use the System File Checker tool to repair missing or corrupted system files
http://support.microsoft.com/kb/929833

Method 2: Hardware troubleshooter
Let’s try running the hardware troubleshooter and check if that helps. Follow these steps to run the troubleshooter.
a) Press the ‘Windows + C’ to activate the charms menu or move the mouse pointer to bottom right corner of the screen and you will get the charms menu.
b) Click on ‘search’ and select ‘settings’.
c) Type ‘Troubleshooting’ and select ‘troubleshooting’.
d) Click on ‘Hardware and Sound’ and select ‘Hardware and Devices’ and click on next to run the troubleshooter.
Method 3: uninstall and re-install the drivers

Follow the steps below to uninstall and re-install the drivers for the Infrared receiver.
Click on Start; in the start search type devmgmt.msc and hit Enter.
Uninstall the device driver.
Unplug the USB cord of the Infrared receiver and reboot. Once it reboots and you are logged in, insert the device back into the USB port. If possible, use a different USB port.