Perhaps your body has a greater need for magnesium at this time and is absorbing some.
In any case, the dose of 1 tsp need not cause loose stools, although it usually does. Just as for some people, it causes liquid stools (diarrhea), for others it might cause no noticeable looseness. Perhaps you should try increasing the doseage to 1 1/2 tsp, or else do 1 tsp in the a.m. and 1 tsp before bed.