Posted from my N900.
Two things:
One, stevomanu is correct. He flashed PR1.3, then restored his PR1.2 backups. These backups only contain rootfs and optfs partitions, and NOT the 2mb kernel/bootloader partition. So, when he flashed PR1.3, it updated his kernel to the PR1.3 one... Which never got removed.
Regarding modified 'hildon-desktop', can you tell me exactly what was modified in the first place, and what -wasn't- afterwards?


Two, and I -just- figured this out last night, the 'backupmenu.item' in /etc/bootmenu.d/ is considered a "configuration" file by the deb packager. This means it doesn't get replaced with an 'upgrade'!
The solution is simple, however:
Run "apt-get remove --purge backupmenu" before installing the new version. This will delete any lingering files, and prevent confusion.

In other news, I added a paypal donate link to the first post, as requested. I, honestly, never thought about it before now.

*whew* - typing this much on my phone's a bit of a pain.