Adhesion problems are usually related to contaminants or residues present on the board prior to coating. By using a suitable cleaning procedure most residues are removed, solving any problems with adhesion.
Silicone contamination can be very difficult to remove and may require multiple cleaning stages depending on what you are using. Cleaning processes can therefore vary depending on the residues or contamination present and so it is difficult for me to offer any advice on your cleaning process without any further information.
If the coating is adhering to the board itself but not to certain components then this is usually a different matter. Commonly, this is due to the components having an "in-built" release agent from the manufacturing process. It is difficult to get anything to adhere to the surface in this case. The legs or any joints of the components however should be unaffected by this matter and will require protection.
I can possibly help further if you can tell me more about your process and what cleaning agents you have already trialled. Do you know if there is a possibility of silicone contamination or are you just trying to avoid this matter? Is the adhesion to the entire board affected?
With regards to the conformal coating you should check whether it is being diluted with any materials and if so is the dilution ratio as specified by the manufacturer? You may have problems with adhesion if the coating is too thick or too thin but this will be dependent on the PCB layout and environmental conditions it is exposed to.
If you need further help on this matter please feel free to contact me direct to discuss in more detail.