Wanting help creating an applescript that is run when the contents of a folder changes
I would create one script that monitors both folders. My language of choice for this is Python. AppleScript is not terribly well-suited to this kind of operation. The basic idea is to listen for FSEvents on the two folders in question, and when one occurs, quickly unschedule the event stream for the other folder, do some conversion and sync operation, then reschedule the previously unscheduled event stream.

The completed script, downloaded here, with modified versions of those scripts you showed me. The MacFSEvents installation is now automatic: 
https://www.dropbox.com/s/oylvewk90ezwb3s/File%20Sync.app.zip?dl=1

Here are the steps to use it:

Extract the applet, right click on it and select "Show Package Contents", open Contents, and Resources, then edit the plist inside with your RTF and MMD folder pairings. You will be able to specify as many pairs as you need to keep synchronized with each other, just stick to the same format as what I used in the plist: One array per pair, each containing two items, the first item being the path to the RTF folder, the second being the path to the MMD folder. You'll see this when you open the plist.

This should work without any issues. The folders will now be watched for any sort of modification, and will have the files converted and transferred to the other folder.