Solved!
My Omega was controlling some outputs with the help of some transistors. The resistors between Omega and the base of transistors were all 1kohm, which might have been too low for Omega capabilities of 4 mA per GPIO. I replaced all of them with 4k7 and it is now working.
I don't even know why I have used such low resitances. I guess I was thinking that if I am not low on power, then why not.