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Danko, Ideally an unretained peak is only affected by packing microstructure (arrangement of the particles) of the bed not the chemistry. The flatter velocity profile of the (unretained) compound the higher the efficiency in a packed bed. If you recall, in CE, an analyte has a flat velocity profile, therefore the efficiency is usually in million plates/meter. In LC, if we ever achieve a bed where the velocity profiles of the solute are flat (rather than parabolic) the plate count can easily be in millions. I know of only one case in LC where a capillary was packed in such a way that the micro-structure of the bed was crystalline, the efficiency was in millions. The reduced plate height were =1, whereas best packed LC, core shell etc. have reduced plate heights between 1.6 to 3. The theoretical limit of reduced plate height is somewhere ~ 0.6 rather than 2 as usually propagated by many authors.All this does not explain the fact that you experience two completely different situations with two differenet stationary phase chemistries.
Best regards