Out of interest, what happens when you deliver a 50Hz 15kHz mode to the encoders but leave them on NTSC?
If these are cheapo Ebay encoders with VGA inputs, i would guess they are not designed for 15kHz input - and you're lucky they work at all. Does the same thing happen when you test a normal 31kHz+ PC video mode only at 50Hz?
If they don't take VGA, what input do they take and how are you combining sync? If they are designed for 15kHz input, test the RGB from a console like a PAL PS1 (or a chipped PS1). It might be that they aren't built to handle 5V TTL sync?