A number of minor issues have been found in the PocketSphinx 0.6 release. We will be preparing a 0.6.1 release to address these, but if you are affected by them, you can track the stable branch of the source code at http://cmusphinx.svn.sourceforge.net/svnroot/cmusphinx/branches/pocketsphinx-0.6 .
For Ubuntu users, source packages and binary packages for Lucid Lynx (10.04 beta) which track the bug-fixes can be found at https://launchpad.net/~dhuggins/+archive/cmusphinx - or simply add ppa:dhuggins/cmusphinx to your list of software sources.