Menu item for Primecoin-qt is shown as PPcoin-qt. PPcoin-qt is the wallet for Peercoin, not fot Primecoin. Please change it.
# grep make_desktop_entry primecoin-qt-0.1.2.ebuild make_desktop_entry "${PN} %u" "PPcoin-Qt" "/usr/share/pixmaps/${PN}.ico" "Qt;Network;P2P;Office;Finance;" "MimeType=x-scheme-handler/primecoin;\nTerminal=false"
Thanks jer, I changed that line to the following and revbumped: make_desktop_entry "${PN} %u" "Primecoin-Qt" "/usr/share/pixmaps/${PN}.ico" "Qt;Network;P2P;Office;Finance;" "MimeType=x-scheme-handler/primecoin;\nTerminal=false" Reopen if there is still an issue.