I think it has nothing to do with the WM Rom. I have stock WM and I use android from the first days. Everything is "voodoo magic", like you said. I tried Ext2, Ext3, Ext4, internal storage, SD, everything and after a couple of months of using android on my Omnia I can say that every thing comes randomly. I had no problem when installing every version, and after couple of days (with Froyo B1 more) I got freeze or SOD, or whatever. Then, every time I say I will be using WM until next beta comes out, but the next day I turn to android again :P and every thing runs perfect for couple of days more until it freezes again or I don't know what happens :rolleyes:.
I hope the new release will come with more battery life, radio and the possibility to move the apps to SD and I see that the randomly problems are less and less now with every version thanks to the devs.