I had the same prob on catchin al monsters in the cave of mt gagazet, i had to catch dark flan but after a while he didn't showed up anymore, then i did the sphere grid with everyone and began walking and then he came back, weird but true.
I also had trouble with finding a Dark Flan. That is really weird how it worked out though, I wonder if Square perposely did that or something. Maybe if you move along on the Sphere Grid the monsters are refreshed, that must also mean that monsters aren't random so maybe that's not the case.