Custom permalinks wreck pagination

I’m totally stumped on this one – and have been for weeks – and would appreciate any help. My site is: http://golovegreece.com/

I can only get Permalinks to work in all scenarios – categories, tags, posts, pagination – only on Default setting. In Custom setting, I can get Permalinks to work for everything… except for pagination – when changing pages using 1,2,3 function – when a 404 error page comes up. In this case, the Custom setting is:

/archives/%postname%/

though I’ve noticed where I have ‘archive’s it doesn’t matter what I have, it’ll work – i.e. work except for pagination.

I have tried a number of possible solutions:

1. Renamed, deleted, recreated .htaccess file.
2. ‘Flushed’ permalink settings.
3. Tried a different theme.
4. Tested permalinks on local server – Custom settings and pagination works fine on local server.
5. Added plug-ins that claim to resolve issue.
6. Deactivated all plug-ins.

Thanks for any advice.