How did you go with setting up the Harmony? They are great remotes, but they do provide some restrictions to use, I find.
I was doing some setup changes with my Harmony 880 as it seems that one of the custom buttons has stopped working. Drat. Anyway...
I'm using the Extended MCE profile available via the Harmony configuration site, which only provides a limited number of IR and Keyboard commands. Most of which are already in use by Windows or MC, and so can't be used for a new command. The command set I am using is called the "Windows Media Center SE" instead of the default "MCE Remote", found by adding a Device on the Harmony site or in their software, such as;
Device -> Media Center PC
Manufacturer -> Microsoft
Model -> Windows Media Center SE
I have had trouble getting passed the "Device" step in my setup in the past, and couldn't add another "Media Center PC" Device today. I know there was some trick to it but can't work it out now. Double drat! I'm pretty sure the only way to select the Extended "Windows Media Center SE" command set if you aren't already using it is to add a new device. Triple drat!
The "Windows Media Center SE" does include the Red and Blue buttons, so they should be available to use for your command, if you can set up or already have a Device using the "Windows Media Center SE" command set.
It doesn't help that the process to get a new command working seems to be convoluted.
On the Remote:Pick an available Command from the Harmony Command set you are using. If there are no unused Commands you will lose the existing functionality of the Command you pick.
OR
Add a new Custom Infrared Command to your Harmony, but that will require a new Infrared code (command) to be assigned to the new Command. Usually, a Harmony remote can learn a new IR code from an original remote or some other device, such as an IR Keyboard. . But there is no guarantee that MC will be able to see and understand the learned IR code, depending on the source of the code. i.e. The new code from another IR remote may use a standard that MC can't read. It is a bit try and see, but I have done that previously.
I set up the existing standard Red and Blue buttons from the "Windows Media Center SE" command set on my Harmony using Custom Buttons for the first time today, rather than creating a new Custom Infrared Command and learning new IR codes. So at that point, I had a Harmony remote that would transmit IR Commands for the standard MCE Red and Blue Buttons.
In JRiver MC:Then in MC, I added two new IR Commands, naming them "Red Button" and "Blue Button", and for each used the "Add Run" button to set MC to launch Microsoft Paint, just for testing. Unfortunately, that didn't work, so I tried Learning the Red and Blue IR code in MC. I received a warning that MC could already handle that IR command because it was an MCE command, but it didn't, so I went ahead with the learning. Both Red and Blue Buttons then worked.
So in answer to your question;
Does MC recognize the mce RED or BLUE buttons?
It should, but it doesn't. However, it can learn these IR codes and then the Red and Blue Buttons work. I also tested the launching of Paint with the Red and Blue Buttons using my standard MCE remote and they worked as well. So the IR codes learned from my Harmony 880 remote are definitely standard MCE codes, but MC didn't recognise them until I had it learn them. Disappointing, but not a major obstacle.