I use Audiosnap to set up transients on real drums and copy them as midi to session drummer a lot for sampling.
Every single time, flams are not detected.  I always have to manually add the second transient of the flam.

Is there a setting or checkbox somewhere to help aid this?

IIRC, you have to play with the audio snap settings that control the detection of transients for best results. 

I forget what the settings are called, but i do remember setting them up so it reads the transients better. The default settings are not always the best. 

I always mess with the % slider, often going to 100% (or is it 0%... I never look at the value I just go till it's enabling most or all of my transients.

I wasn't aware that there were settings on how many transients were 'detected'.  I thought the settings were all for which were 'enabled'.
Perhaps I was looking at things improperly.