I am experiencing problems with one-dimensional Blue Native PAGE: It seems that proteins in the rage of 300 - 600 kDa are not properly transferred onto the PVDF membrane during Western Blotting of a BN-PAGE gel.
Those are fairly large proteins, and the CBB in BN-PAGE is a weaker mobilising agent than SDS. You could try lower %T gels, stabilised with agarose (doi:10.1006/abio.1995.1004) or you could incubate the gel with 0.1% SDS (perhaps at 50 °C) before blotting. The latter of course works only if your antibody can detect denatured proteins. Do not use methanol in your transfer buffer.