Using both the import function and the API, I am finding that the last phone entry entered is replacing the primary location's phone entry, with no trace of the other one.
From the import menu:
FAX => Work -Fax -Phone
PHONE => Work -Phone
But the contact entry shows "fax" only.
This is also happening with the API: If I include a phone and a phone_type entry in $params, it gets set correctly. If I try to crm_update_contact with phone and phone_type->fax my entry gets overwritten.