Calibre comes out with a release every week - trying to find out what makes your collection of books take forever now vs. year ago is non-trivial. People who do some investigation and highlight specific behavioral differences between now and past releases tend to get help, but general comments that things are slow without any actionable examples rarely initiates any changes.
Both pdf and chm can vary radically from document to document as well, so it's quite possible that you're now attempting conversions of documents that have always been slow - had you tried those same particular docs a year ago you may have seen slowness then.
Back-releases of Calibre are available on the download site:
http://sourceforge.net/projects/calibre/files/
You can download the release from a year ago if you want to investigate further and see what portion of the conversion is taking longer. If you can document a difference then it will generally be addressed.