Unreliable Folder Action
In my and others' experience, Folder Actions are unreliable, especially with large numbers of changes. So the problem you're facing is not specific to your system, but a rather common one.

I suggest you rewrite your script into one that receives a folder as input, and performs the Markdown transformation on all files within. Have it trigger automatically whenever a file is written to by a launchd job, with the parent folder specified in the WatchPaths rule.

Since most programs on OS X perform atomic saves and thereby replace the previous file instead of simply modifying its contents, the folder will also be updated and the job will be triggered reliably.

Markdown transformation also shouldn't be too time consuming, and you can always ensure only to transform files using your script that were changed in the last X minutes.