I compiled the development-sources, using mostly the standard config info, to troubleshoot a usb device problem I was having with gentoo-sources. The compile worked well, the system boots with no obvious errors. When I log into gnome, my (reversed) mouse buttons do not function correctly. I cannot select anything reliably. When I managed to grab the mouse settings application, and un-reversed the mouse buttons, the mouse began working correctly. I changed proc type (athlong), network driver (natsemi) and turned all possible options from modules to built-ins. The balance of the config was the stock config in the development-sources ebuild, as far as I can tell. Reproducible: Always Steps to Reproduce: 1. Reverse mouse buttons in gnome under stock gentoo-sources kernel 2. Emerge development-sources. Make minimum required changes for my architecture. 3. Re-boot to 2.6 kernel and log in. Actual Results: Mouse pointer tracks correctly. Mouse buttons on desktop pop open windows (terminal, nautilus). Mouse button clicks on menu items open menu, but do not select actions. Repeated button clicks will eventually select some items. Expected Results: Correct mouse button operation. Gentoo Base System version 1.4.3.10 Portage 2.0.49-r10 (default-x86-1.4, gcc-3.2.3, glibc-2.3.2-r1, 2.6.0-test6) ================================================================= System uname: 2.6.0-test6 i686 AMD Athlon(tm) XP 2500+ ACCEPT_KEYWORDS="x86" AUTOCLEAN="yes" CFLAGS="-O3 -march=athlon-xp -funroll-loops -fprefetch-loop-arrays -pipe" CHOST="i686-pc-linux-gnu" COMPILER="gcc3" CONFIG_PROTECT="/etc /var/qmail/control /usr/kde/2/share/config /usr/kde/3/share/config /usr/X11R6/lib/X11/xkb /usr/kde/3.1/share/config /usr/share/texmf/tex/generic/config/ /usr/share/texmf/tex/platex/config/ /usr/share/config" CONFIG_PROTECT_MASK="/etc/gconf /etc/env.d" CXXFLAGS="-O3 -march=athlon-xp -funroll-loops -fprefetch-loop-arrays -pipe" DISTDIR="/usr/portage/distfiles" FEATURES="sandbox ccache autoaddcvs" GENTOO_MIRRORS="http://gentoo.inode.at" MAKEOPTS="-j2" PKGDIR="/usr/portage/packages" PORTAGE_TMPDIR="/tmp" PORTDIR="/usr/portage" PORTDIR_OVERLAY="" SYNC="rsync://rsync.gentoo.org/gentoo-portage" USE="x86 apm crypt cups encode gif libg++ mad mikmod nls pdflib spell truetype xml2 xv zlib gdbm berkdb slang readline tetex svga tcltk sdl gpm tcpd pam libwww ssl perl python esd imlib motif cdr acpi alsa arts avi bonobo cpus doc foomaticdb gnome gphoto2 gtk gtk2 ipv6 joystick jpeg kde mozilla mpeg ncurses oggvorbis oss opengl png qt quicktime samba scanner usb X xinerama xmms"
I assume that this happens with all X11 based applications, not just Gnome? Can you please check your /var/log/XF86*... to see if there is anything wrong / failing there?
Please see comment #1 - if you still experience this problem on the latest 2.6 series kernels please reopen this bug.