When comparing results obtained by methods based on different principles (ex. VNT vs. ELISA, IFI vs. ELISA, CFT vs. ELISA), it is practically impossible to obtain perfect test agreement, unless very strongly positive and perfectly negative samples are used.
This is also true when comparing cELISA and iELISA results. The polyclonal nature of serum means that it contains populations of IgGs with different affinities for different antigens, each antigen with many epitopes. Each technique detects these populations to a different extent. Sera close to the cut-off will show more discordant results, as they contain more limited quantities of each type of antibody.