Is this from loading a previously saved file or when creating a new file?
mev_title_continue_fileselected has some fallback code if the load fails which warps you to a specific spot (indoors area with coordinates set to the center of the lab), cc_intro_startgame is what sets your initial position from a new savefile - this is the same coordinates as the fallback when loading though.
To capture all room transitions in the debug messages you could open room_goto_fade and room_goto_fade_dontdestroy and add a line at the start (before the room is changed), this should point out if there's any room transitions happening so fast you don't get a chance to react:
show_debug_message(tsprintf("Room change % --> %",room_get_name(room),room_get_name(argument0)))
Did you add the debug message that prints the player's position after loading I suggested last time?