Intermediate roller links the inking unit to the dampening system, it helps in getting good ink water balance quickly.
It can be disengaged if you are running low coverage jobs or metalics.
This will prevent emusification of the ink.
When you are getting ink on the water pan roller, its more likely to be your chemistry.
Pan roller should remain clean if your roller setting and pressroom chemistry is good.
Are you adding alcohol and fountain solution in the water?