I made my own VGA to Scart cable, and it works fine with most cores. However, ST core only gives me black screen/ no signal. Previously i used it with VGA from analog IO board, scandoubler was on so it was 31khz.
Now made settings to mister.ini with composite sync 1 and everything else 0, however i think ST core is still trying to output 31khz.
I am still very new to Mister, where can i change individual core settings? Thank you. 
Aside from the ini's "forced_scandoubler" setting, each core also have individual settings for scandoublerfx. Sometimes they are even just called "scanlines." If any of those are enabled the analog out won't work with 15khz displays. It will be in the video options (NOT the video filters) of the core itself, so you might need another monitor (preferably an HDMI one) to see what you are doing and change the setting back.
That's what i was afraid of, because Mister doesn't seem to save my settings. If i can't modify core startup settings i will need to connect another display every time i want to play some ST games.
There's some kind of files in the SD card config folder that hold the menu settings for each core. Not sure exactly what they are called but should have AtariST in the name. Deleting those should return you to defaults.
Have you tried the following ?
[AtariST]
forced_scandoubler=0
vga_scaler=0
composite_sync=1