Yes, it happens to all of our tandems (although you'd need to quantify 1/2 a cup -- 1/2 of what type of cup?) and, yes, it's an annoyance.
As to where the water gets in, IMHO I believe it sneaks in from a variety of places. On the road tandems, most likely sources for our water penetration has been:
1. Front eccentric -- being fed by the rooster tail coming off the front tire, I suspect some water seeps in between the eccentric and the bottom bracket shell, and then works it way into the boom tube.
2. Rear BB -- pulled into BB shell between the axle and seals by capillary action as the axle flexes under the extra load from the front cranks and then, like the front end, the water moves into the boom tube.
3. Rear chain stay openings -- those little holes near the rear drop outs. Water can get in there, move forward to the rear BB and then move into the Boom tube.
Water gets into many of the same places on single bikes, but they don't have that boom tube to act as a reservoir and the water usually runs back out.