I came across a good discussion of how to handle a bad reference in a job-search-related blog.
It highlights a very key point when seeking critique in any situation - 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.
The approach they describe shows you to be a mature professional, and even if it doesn’t change 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 seeking critique:
And for the blog entry on handling a bad reference: