You just need to select all the backlinks in your SEO SpyGlass project, copy them to clipboard and then click Edit -> Paste Link Partners. Each domain will be present only once in your workspace.
But I did´t understand that, or rather I could not repeat it. Is it possible to explain it in other words?
The suggested workaround was to open LinkAssistant ( http://www.link-assistant.com/linkassistant ) and paste the partners copied from SEO SpyGlass into a new project. That way each domain will be pasted only once (LinkAssistant will cut off 'duplicate partners') and you will have a list of unique domains.