Actually I got this problem too, only for when player never visited any pokécenter yet.
Open the file metadata.txt in the PBS folder and near the beginning of the file you'll find a line with "Home=x,x,x,x". First x is the map ID, second and third are the position on the map where the player will respawn (usually it's in front of Mom in regular games) and last x is the player direction (8 is facing up, other values are 2, 4 and 6 (I don't remember the directions, so try yourself)).
To get the position in the map, just open it in RMXP and put your cursor above the tile you want to be the respawn place. Coordinates of the tile will be displayed on the bottom right of RMXP window.