Today's RAM is synchronous, meaning the signals are operating to a clock signal. But nothing in the world can work all exactly at the same time. So while MB A may have a longer delay on line X but MB B may have a longer delay on line Y. Then this set of RAM may met its worst case in that MB. And it seems in your case it works mostly, then it is just a minor incompatibility.
Today's RAM is very cheap, about $1/chip. Manufacturers cannot afford to test them extensively like in yesteryears. This set of RAM may have some weakness too.