How long has the beer been in the bottles? What temperature are you keeping the bottles at?
I also bottle in 1 liter fliptops and in my experience they need more time to carbonate. Also, one has to be real careful to seat the top absolutely straight on the bottle mouth; if they are just slightly tilted, the top may not completely seal your bottles
Primary - none
Secondary - none
Bottled - APA, robust porter, hefeweizen