Same problem:
*****Note: under a new, test user this problem does not occur****
======================

After upgrading to 9.04 amd64 from 8.10 amd64 dual monitor not xinerama, compiz fails to run.

I 8.10 compiz had to be started by a script, to wit:
 compiz --display :0.0 --only-current-screen --replace &
 compiz --display :0.1 --only-current-screen --replace &

After upgrading and installing glib2.0 patch (https://bugs.launchpad.net/bugs/346964)
and reloading compiz, it failed to start.

As a test, I created a new user to test compiz⋯where it worked.

I ran this in the terminal:
 compiz --display :0.1 --only-current-

screen --replace emerald &

And it crashed the window manager on display :0.0 (results below)

I started Compiz Fusion Icon, and used it to attaemp to start compiz, and it crashed the window manager.

How can I get Compiz to function properly?

terminal result from compiz attempt:

~$ compiz --display :0.1 --only-current-screen --replace emerald &
[1] 16448
ljohnson@KISE-005:~$ Checking for Xgl: not present.
xset q doesn't reveal the location of the log file. Using fallback /var/log/Xorg.0.log
Detected PCI ID for VGA:
Checking for texture_from_pixmap: present.
Checking for non power of two support: present.
Checking for Composite extension: present.
Checking screen 1Comparing resolution (2560x1600) to maximum 3D texture size (8192): Passed.
Checking screen 2Comparing resolution (1440x900) to maximum 3D texture size (8192): Passed.
Checking for Software Rasterizer: Not present.
Checking for nVidia: present.
Checking for FBConfig: present.
running under gnome seesion, checking for gnomecompat
Checking for Xgl: not present.
/usr/bin/compiz.real (core) - Error: Couldn't load plugin 'emerald'
/usr/bin/compiz.real (core) - Warn: Plugin 'core' already active
/usr/bin/compiz.real (cube) - Warn: Failed to load slide: /usr/share/gdm/themes/Human/ubuntu.png
/usr/bin/compiz.real (cube) - Warn: Failed to load slide: /usr/share/gdm/themes/Human/ubuntu.png
*** glibc detected *** /usr/bin/compiz.real: double free or corruption (!prev): 0x0000000002278620 ***
======= Backtrace: =========
/lib/libc.so.6[0x7fe7779f5cb8]
/lib/libc.so.6(cfree+0x76)[0x7fe7779f8276]
/usr/lib/libGL.so.1[0x7fe77982012a]
======= Memory map: ========
00400000-0043c000 r-xp 00000000 08:31 15149020 /usr/bin/compiz.real
0063b000-0063c000 r--p 0003b000 08:31 15149020 /usr/bin/compiz.real
0063c000-0063d000 rw-p 0003c000 08:31 15149020 /usr/bin/compiz.real
01ebc000-027aa000 rw-p 01ebc000 00:00 0 [heap]
7fe771e5e000-7fe771e6a000 r-xp 00000000 08:31 4538587 /lib/libnss_files-2.9.so
7fe771e6a000-7fe772069000 ---p 0000c000 08:31 4538587 /lib/libnss_files-2.9.so
7fe772069000-7fe77206a000 r--p 0000b000 08:31 4538587 /lib/libnss_files-2.9.so
7fe77206a000-7fe77206b000 rw-p 0000c000 08:31 4538587 /lib/libnss_files-2.9.so
7fe77206b000-7fe772075000 r-xp 00000000 08:31 4538589 /lib/libnss_nis-2.9.so
7fe772075000-7fe772274000 ---p 0000a000 08:31 4538589 /lib/libnss_nis-2.9.so
7fe772274000-7fe772275000 r--p 00009000 08:31 4538589 /lib/libnss_nis-2.9.so
7fe772275000-7fe772276000 rw-p 0000a000 08:31 4538589 /lib/libnss_nis-2.9.so
7fe772276000-7fe77228c000 r-xp 00000000 08:31 4538584 /lib/libnsl-2.9.so
7fe77228c000-7fe77248c000 ---p 00016000 08:31 4538584 /lib/libnsl-2.9.so
7fe77248c000-7fe77248d000 r--p 00016000 08:31 4538584 /lib/libnsl-2.9.so
7fe77248d000-7fe77248e000 rw-p 00017000 08:31 4538584 /lib/libnsl-2.9.so
7fe77248e000-7fe772490000 rw-p 7fe77248e000 00:00 0
7fe772490000-7fe772498000 r-xp 00000000 08:31 4538585 /lib/libnss_compat-2.9.so
7fe772498000-7fe772697000 ---p 00008000 08:31 4538585 /lib/libnss_compat-2.9.so
7fe772697000-7fe772698000 r--p 00007000 08:31 4538585 /lib/libnss_compat-2.9.so
7fe772698000-7fe772699000 rw-p 00008000 08:31 4538585 /lib/libnss_compat-2.9.so
7fe772699000-7fe7726c8000 r-xp 00000000 08:31 4538374 /lib/libpcre.so.3.12.1
7fe7726c8000-7fe7728c7000 ---p 0002f000 08:31 4538374 /lib/libpcre.so.3.12.1
7fe7728c7000-7fe7728c8000 r--p 0002e000 08:31 4538374 /lib/libpcre.so.3.12.1
7fe7728c8000-7fe7728c9000 rw-p 0002f000 08:31 4538374 /lib/libpcre.so.3.12.1
7fe7728c9000-7fe77290d000 r-xp 00000000 08:31 15147259 /usr/lib/libgobject-2.0.so.0.2000.1
7fe77290d000-7fe772b0c000 ---p 00044000 08:31 15147259 /usr/lib/libgobject-2.0.so.0.2000.1
7fe772b0c000-7fe772b0d000 r--p 00043000 08:31 15147259 /usr/lib/libgobject-2.0.so.0.2000.1
7fe772b0d000-7fe772b0e000 rw-p 00044000 08:31 15147259 /usr/lib/libgobject-2.0.so.0.2000.1
7fe772b0e000-7fe772b0f000 rw-p 7fe772b0e000 00:00 0
7fe772b0f000-7fe772b4b000 r-xp 00000000 08:31 4538534 /lib/libdbus-1.so.3.4.0
7fe772b4b000-7fe772d4a000 ---p 0003c000 08:31 4538534 /lib/libdbus-1.so.3.4.0
7fe772d4a000-7fe772d4b000 r--p 0003b000 08:31 4538534 /lib/libdbus-1.so.3.4.0
7fe772d4b000-7fe772d4c000 rw-p 0003c000 08:31 4538534 /lib/libdbus-1.so.3.4.0
7fe772d4c000-7fe772d6c000 r-xp 00000000 08:31 15150053 /usr/lib/libdbus-glib-1.so.2.1.0
7fe772d6c000-7fe772f6c000 ---p 00020000 08:31 15150053 /usr/lib/libdbus-glib-1.so.2.1.0
7fe772f6c000-7fe772f6d000 r--p 00020000 08:31 15150053 /usr/lib/libdbus-glib-1.so.2.1.0
7fe772f6d000-7fe772f6e000 rw-p 00021000 08:31 15150053 /usr/lib/libdbus-glib-1.so.2.1.0
7fe772f6e000-7fe772f75000 r-xp 00000000 08:31 4538594 /lib/librt-2.9.so
7fe772f75000-7fe773174000 ---p 00007000 08:31 4538594 /lib/librt-2.9.so
7fe773174000-7fe773175000 r--p 00006000 08:31 4538594 /lib/librt-2.9.so
7fe773175000-7fe773176000 rw-p 00007000 08:31 4538594 /lib/librt-2.9.so
7fe773176000-7fe77317a000 r-xp 00000000 08:31 15151815 /usr/lib/libgthread-2.0.so.0.2000.1
7fe77317a000-7fe773379000 ---p 00004000 08:31 15151815 /usr/lib/libgthread-2.0.so.0.2000.1
7fe773379000-7fe77337a000 r--p 00003000 08:31 15151815 /usr/lib/libgthread-2.0.so.0.2000.1
7fe77337a000-7fe77337b000 rw-p 00004000 08:31 15151815 /usr/lib/libgthread-2.0.so.0.2000.1
7fe77337b000-7fe77337e000 r-xp 00000000 08:31 15150737 /usr/lib/libgmodule-2.0.so.0.2000.1
7fe77337e000-7fe77357d000 ---p 00003000 08:31 15150737 /usr/lib/libgmodule-2.0.so.0.2000.1
7fe77357d000-7fe77357e000 r--p 00002000 08:31 15150737 /usr/lib/libgmodule-2.0.so.0.2000.1
7fe77357e000-7fe77357f000 rw-p 00003000 08:31 15150737 /usr/lib/libgmodule-2.0.so.0.2000.1
7fe77357f000-7fe7735db000 r-xp 00000000 08:31 15148299 /usr/lib/libORBit-2.so.0.1.0
7fe7735db000-7fe7737db000 ---p 0005c000 08:31 15148299 /usr/lib/libORBit-2.so.0.1.Aborted
metacity: Unknown option --only-current-screen
~$