Here is what I do:
Remove any rinse aid like jet-dry from your machine.
I run the bottles in the dishwasher with PBW on the pots/pans setting and heat turned on.
Once the bottles have cooled, I remove them to the counter and spray the dishwasher tines with star san. I then use the vinator with starsan and quicky give the bottles one or two squirts, then set them back into the washer neck-down to drain while I transfer my beer to the bottling bucket.
This process is extemely quick, easy, uses a minimum of cleaner, and I've never had any issues with it.
the Starsan/vinator may actually be overkill, but it takes less than 10 minutes to do with 22 0z. bottles, and uses less than a quart of star-san. Cheap insurance ...
Pez.