Dan I just programmed a FT-8800 and I have some interesting results. I tried to make channels as P (preferred for scanning) since the list I imported has quite a number of repeaters and simplex freq. I also set the scn.msm to msm. and scan mode to msm However I am still scanning all memories! I downloaded the radio using Bob Freeth software and discovered that the Preffered bits are set for Hyper Memory 2 mostly correct, Hyper Memory 1 mostly wrong ( missing quit a few, some random ones set). the other hyper memories are not set at all.
I have attached before and after files. The ones that do not say new are the one where I imported my radio, then the CSV file, marked the channels as pref.
The one with new in the name were done by reading the radios using bob Freeth's software, correcting the issues, writing them back out to the radio and testing them, then reading them back in using chirp. This should give you two set of files in your format to compare the differences.
Allan WB5QNG