I came across a good discussion of how to handle a bad reference in a job-search-related blog. While the blog seems to have been closed, here was the essence of their point:
A key point when seeking critique in any situation is this – don’t get defensive. As soon as you start to try to explain why something isn’t a problem, you shut down the input you might have received. And in this case, where there is already (apparently) a relationship issue, you can actually make the situation worse.
You want to show that you are a mature professional, and even you aren’t successful in changing the negative perception of PAST performance, it can help that former boss to see you in a new light.
I wrote a related piece some time back on the more general issue of how best to seek critique.
Try it, and let me know what happens. Leave a comment here.
And while the blog item I originally read no longer exists, here’s another piece on the subject that gives good advice on the topic.