It sounds like you have a problem with how you have formatted your CSV file and headings.
It is not really a Toolset issue, but I don't mind taking a look for you.
Why don't you upload your csv file somewhere like dropbox or Google drive and share the link with me? I'll mark your next reply as private so that only I see the link (you can ignore the template asking for your WordPress site credentials).
I re-ordered the columns so that you had all the standard WP fields first then your custom fields (matching the order shown in the sample.csv file in the examples folder of the csv importer plugin) and tried again and it worked.
I didn't notice that documented anyway, but testing that it seems to resolve the problem, if you want to give it a try.