I've created a user importer attached to a content type, with file upload fetcher, CSV parser, and user processor that takes email address and user name values and sets the email address as unique value. User processor settings are to make user active, give one additional role out of a possible five, and not update existing users. I've carried out a test import a few times, and each time all imported users are assigned all possible roles, including the unauthenticated role created by Logintoboggan.
I've tried changing the processor to assign 0 extra roles instead of 1, and changing the data being imported, but the problem remains.
Versions are Drupal 6.17, Feeds beta 2, Location_Feeds 6.x-1.1, Aegir 0.4-alpha8, php 5.2.6-1, CTools 6.x-1.6, Apache 2.2.9, Logintoboggan 6.x-1.7. Node processor custom-patched from #632920: Inherit properties from parent feed node (taxonomy, author, OG, language) but that shouldn't affect this. Let me know if you'd like any more info. Couldn't find anyone else with the same error, and I've tried drush cc all this time round, so it's not that!