We have an import that we do a few times a year that I set up about 2 years ago. Until today, it's never had an issue. We are using v4.6.3, and the last time we did it we were using a 4.5.x version.
When importing households, we have some custom relationships defined. They are Individual to Household relationships. These relationships do not show up in the selector for the mapping the imported data. Some relationships DO show up; Household member and Head of Household, plus two other relationships in which contact a type is not set.
The relationships that don't show up are useable in all other contexts that I have tried. They are enabled. I have gone so far as to compare the relationship type records in mysql and I see no obvious issues.
I've also searched the Jira to see if there's a known issue but I don't see any.