I am having a similar issue.
I can't compare with a previous version, but it seems that after so many times (about an hour's worth)the ancestry.com merge slows down significantly.
However, my work around is to disengage and get out of the software totally and then get back in. The original speed seems to return.
Sorry, I don't have technical details with regard to speed and such. It is merely my sense of time and the ability to do more things between downloads.