To confirm; this is RO/DI water at 0TDS?
How quickly does it develop? How often do you clean out the bucket, in other words?
Is the lid on tight (and, if so, how are the cables passed through it)? Or does it just rest on the top, with the cables coming out between the lip of the bucket and the lid?
Where is the tank located in relation to the bucket, and where is the output line of the ATO? It's possible that when the ATO shuts off, it draws in a little bit of saltwater in a back-siphon. This could cause the RO/DI water to develop some debris.