/var is on rootfs, not on eMMC. You say in the first post that you "flashed the OS and removed alarmed". If you flashed the OS you didn't have to remove alarmed (because it doesn't come with the stock firmware), so at this point I'm not sure what you did and what you didn't do.

I would bet that flashing the combined image (aka rootfs) would necessarily replace /var/cache/alarmd/alarm_queue.ini with whatever comes as default (i.e. definitely not including anything alarmed-related, just HAM, modest, etc.)

If anybody happens to read this and be about to reflash his/her N900 it would be nice if this could be confirmed.