not sure i understand about the empty pot.
when i wrote the utility my thinking was that putting soil and water in the pots and doing the test to find the pots was something you would have to do only once. for some reason, rarely, plant tycoon seems to move where it keeps the pots in memory.
with that in mind, if the watering is not working right try refinding the pots with the filling with soil and watering them pot finder thingie.
Good luck,
-Borg