atop 1.25 released on April 30, 2010. Follow URL for the release notes. There's a reference of one fixed buffer overflow happened on some conditions (long uptime) in the atop codebase, so this release probably can be a security update. Please also note item d) in the release notes. Portage now unmerges both /usr/bin/atop and /usr/bin/atop-version if atop 1.25 has been installed with atop-1.24-r1.ebuild renamed to atop-1.25.ebuild. Reproducible: Always
1.25 is in the tree. Thanks for reporting.