At the back of the machine under the lid there are usually 2 or three water solenoid valves.
These valves operate depending on what part of the program is running. One of these will be the conditioner water valve, if it has failed you will not get water going to the conditioner part of the soap dispenser hence no conditioner will be flushed out.
When you say you cleaned out the soap dispenser did you take it fully apart as crud gets stuck in the top hat part and prevents the syphoning action, this will need to be cleaned out fully.
To test the water solenoid valves you check the continuity through the valve winding it should be a fairly high resisitance 30K or so, or if you know what your doing apply a seperate 240V supply to the valve.