A solution for people that use a custom kernel (Like titan's, Jebba's, or selfmade) :
I had the problem that mer did not boot after using the kernel-flasher. After i talked to titan, i know now why.
There are some modules that are missing in mer. So just make a copy from the folder /lib/modules/2.6.28maemo-omap1 on the N900 and put it in the mer sdhc /lib/modules.
Worked fine for me.