Firstly, I apologize in advance for my poor bug report. I'm not really in to programming.
I'm running Fedora 11/GNOME with Scim and Anthy installed from the official repositories of my distribution. (Version: 1.4.8 Release : 3.fc11)
The primary language I use is Greek, which requires one dead key for accent, and optionally compose for special characters. I use English and Japanese too. In Qt apps (and KDE), with SCIM installed (not necessary activated) the dead keys and compose can't be used, the accent mark is placed as an individual character before the letter that it should accent -GTK apps have no problem even with SCIM activated. Same occurs to users from Iceland that also need dead keys. Removing every single scim package from the system solves the problem. I didn't try just to remove the Qt-related ones but I believe the "bug" is in these packages. Running the Qt apps as root user bypasses the "bug" but SCIM won't load.
At first somewhat related discussions:
http://bugs.scribus.net/view.php?id=1908
https://bugzilla.redhat.com/show_bug.cgi?id=468590
https://bugs.kde.org/show_bug.cgi?id=180506
http://bugs.gentoo.org/131644
And then my solution: QT_IM_MODULE=scim has this problem, QT_IM_MODULE=xim works fine.
My package version (Gentoo): x11-libs/qt-3.3.8b-r1, x11-libs/qt-core-4.5.1, app-i18n/scim-1.4.9, x11-base/xorg-server-1.5.3-r6
My configuration: environment LANG=cs_CZ.UTF-8, XkbLayout "en,cz", /SupportedUnicodeLocales = en_US.UTF-8,cs_CZ.UTF-8 in /etc/scim/global.
Demetris, thank you for the report. Are you still seeing this problem?