You explained it correctly. If a scripted movement is getting cut off, you need to put a wait command after the move command. It will take some trial and error to get the proper amount of wait time though.
Spiff: Here's a clear cut way
1) go into the correct password fork
2) add the event "Change variable"
3) select a new variable and name it
4) increment the variable by one (i.e. have it on set and 1)
5) go to the door event
6) click create new page
7) check the variable check box and select the new variable and set the value to 1
8) make sure that it's representing a blank space
9) add any teleportation if nessecary
This variable can be reused for future events in the dungeon (I recomend having one of these variables for each dungeon you do.) You can make anyone disapear this way.