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I can't seem to make this work (or find info on the internet on the issue). Are there any additional settings when creating initramfs with the root filesystem on lvm?

This should be the settup:

 /boot -> bootable ext3, containing the kernels
 / -> root on lvm, jfs
 /usr -> usr on lvm, jfs
 /var -> var on lvm, jfs

I am working with debian squeeze, kernel 2.6.32-5-amd64, lvm2.

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I don't work much with Debian, but in general, you need to make sure your initramfs environments includes all the necessary kernel modules -- that's typically the LVM modules, the appropriate filesystem modules (jfs), and whatever block device drivers (e.g., a scsi driver, etc). – larsks Sep 12 '11 at 13:27
I don't use debian, but i guess it should have a directory /usr/share/initramfs-tools and there there is a file called modules where you can add modules to be included. Your problem are the lvm modules. Then you can update the initram image - check here: kernel-handbook.alioth.debian.org/ch-initrd.html – Feiticeir0 Sep 12 '11 at 13:41
It should just work automatically if you have installed everything with the Debian tools in the Debian way (no custom kernel etc). – snap Sep 12 '11 at 13:59
Are you sure that it is about LVM and not about JFS? Do you have any relevant boot messages? There seems to be a JFS related Debian bug report which could be related at: bugs.debian.org/cgi-bin/bugreport.cgi?bug=596391 – snap Sep 12 '11 at 14:07
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Do you install this setup from debian-installer? If yes, this should be a bug, which you should report[1].

If your change your system with some external tool like a live-cd or else, then you must run inside the fully mounted changeroot environment ( be aware of /proc & /dev in changeroot) 

# update-initramfs -u -k all

I'm not sure about using jfs as root filesystem, but this should run well.

[1] http://www.debian.org/Bugs/Reporting

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