I use flip top bottles exclusively for bottling my second ferments. I have noticed this same behavior. For some reason once in a while there will be one or a series of bottles that just taste completely flat. Normally what I notice is after cleaning my continuous brewer, the first bottles I draw are fairly fizzy but not especially tasty. The bottles drawn after a few days are the best tasting and most fizzy. Then toward the end of the two week period they are still fizzy but the taste starts to get a little off from the dead yeast accumulation at the bottom of the brewer, so then I clean it out.
Some people like to 'prime the bottle for carbonation'. That could be a little bit of sugar placed in the bottle for example. Or it could be some fruit added for the second ferment. I usually put a slice of ginger, a gogi berry, and some elderberries. Supposedly the 2F bottles can explode. I have not had that happen yet, but I have had a few that when I popped the top half the bottle's contents literally went a good 18 inches into the air.