Reverse Phase Chromatography
I am just wondering how it comes that 60-100% methanol fractions from MCI gel CHP20P eluted very early on C8 column?!


The gel you are using seems to be a porous divinyl benzene / styrene resin.  The aromatic groups of the resin may interact more strongly with aromatic side chains on your molecule (e.g. Y residues) than does the aliphatic C8 groups of the reversed-phase HPLC column you are using.  

"Hydrophobic" vs. "hydrophilic" is a very useful axis for understanding solute interactions with stationary phases, but unfortunately not everything can be collapsed into this single-variable scale. 

Another possibility is that residual solvents or very large amounts of co-solutes are interfering with the RP-HPLC method you are using, causing premature elution.  As an extreme example of what I mean, imagine if you injected a few &mu;L of chloroform along with your sample in the RP-HPLC method.  The chloroform would prevent column binding and cause premature elution.  Now, it's unlikely your samples have chloroform, but they could have large amounts of methanol or other "solvent-like" impurities. 

These are just general points; unfortunately I can't be sure that either is the precise source of your particular problem, without more (and more clearly presented) information on your former method from five years ago, your method today, and the differences in observed vs. expected results.