I know in fallout 3 they updated on the 3rd day and then on the 4th day and then start over again. This does not appear to happen in fallout new vegas.
I looked in the geck for "merchant respawn" in the settings and i found a setting for day 1 and day 2, day 1 had a value of 0 and day 2 had a value of 3.
this might be whats messing things up.
I dont have my copy of fallout 3 any more so i cant check it in its GECK, but if someone could go into the fallout 3 GECK and check those two values to see if its those that have been messed up (seems like the most logical answer) id be very grateful.