Ganard, suspect that you are too quick with switching off the batteries.
Extract from A330 should be similar:
On the APU page of the SD:
- a short time after the APU speed decreased to 7%, the FLAP OPEN indication goes off.
- 30 seconds after the APU speed decreased to 7%, the APU speed and EGT indications show XX (amber).
NOTE: Switching the Batteries OFF before the APU air inlet flap is completely closed may cause smoke in the cabin during the next flight, therefore wait as long till SD shows crosses XX in amber to be sure the shut down process is finished.
So waiting 60 secs minimum after seeing flap OPEN indication disappear and then deselect BATT1, BATT2 and APU BATT should improve your lot...
Of course this maybe completely different to the Baby Buses..