Your code looks ok. I'd change some syntax details to make it simpler:
function FA(){
X += Y;
setTimeout("FA()",1000);
}
function FB(){
Y++;
}
i think the problem may be somewhere in the code you didn't post. it looks like you add Y value twice, so tripple-check if you call FA again. It would cause what you are experiencing now (you may have TWO timeouts).