The OpenAppID feaure was added by the Snort VRT about 2 or 3 years ago if I recall correctly. Shortly after it was introduced I incorporated support for configuring it within the pfSense Snort package. However, there is much more to using OpenAppID than simply checking the box in the GUI. You must create your own custom rules to actually implement Application ID inspection. There are a critical set of OpenAppID stems that come from the Snort VRT via the updates, but they are not all that you need to actually implement OpenAppID. So if you enabled the feature without also creating the necessary custom rules for traffic inspection, it is actually doing nothing.
There have been several reports of errors within the OpenAppID stems that are packaged in the Snort VRT signature updates. Unfortunately with Snort, when it encounters any kind of syntax error in rules or other items it is loading, it will error out and quit. Suricata will log an error, but then skip the errant rule and continue loading the others. So what is likely happening with OpenAppID enabled is Snort hits one of those random errors that seem to get into the OpenAppID stems update and quits. Because Snort is so terribly chatty and fills the system log with essentially every action it takes when you enable normal logging, the pfSense package always starts Snort with the "quiet" switch to cut down on all the log noise as Snort starts. You can disable this feature and turn on the verbose logging by toggling a parameter on the GLOBAL SETTINGS tab.
Here is how I think this might be happening to you. Enabling the OpenAppID preprocessor will cause Snort to load that piece of code and to download the OpenAppID stem updates along with the regular VRT rules update. Snort will then start to load and process the updated files. If OpenAppID is enabled, and the OpenAppID stem files have any errors in them, Snort will log the error and die. The error will only show up in the system log on pfSense if you have turned on verbose Snort logging (that GLOBAL SETTINGS parameter I mentioned earlier). So if Snort encounters an error in the rules or OpenAppID updates, it will just seemingly die for no reason when the "quiet" switch is enabled. As I mentioned, using the "quiet" switch is the default on pfSense otherwise you get several hundred lines of Snort start-up text in the system log.
Bill