I was getting a very similar error...
Duplicate entry '14-6' for key 'PRIMARY'Duplicate entry '14-6' for key 'PRIMARY'
SQL=INSERT INTO
#__finder_links_terms4
`#__finder_links_terms4` (link_id
`link_id`,term_id
`term_id`,weight
`weight`) SELECT 14,term_id
`term_id`, ROUND(SUM(context_weight
`context_weight`), 8) FROM#__finder_tokens_aggregate
`#__finder_tokens_aggregate` WHEREmap_suffix
`map_suffix` = '4' GROUP BYterm
`term` ORDER BYterm
`term` DESC
...and solved this by clicking the 'Clear Index' button at the top. After that I was able to index my files.