There shouldn’t be any limit on the number of fields.
Do you actually have a post with those fields? WP is finicky – it doesn’t consider the fields to “exist” until there’s at least one published post containing these fields, so in some cases you may need to create a dummy post.
If the fields don’t exist, in TurboCSV you should still be able to import them as ‘new’ custom fields rather than ‘existing’.
If that doesn’t help, feel free to send a login and some instructions to reproduce the problem, and I’ll be happy to take a look for you.