I was actually hoping there was some wb config file in which i could manually set the palette properties ... or something simillar.
You really would be better off using Workbench3.1. Infact you could install 3.1 over the top of what's already there. As I said earlier, Workbench2 prefs isn't playing well with Kickstart3.
But like mfilos states in his post, try FullPalette from aminet first, or something similar.
Or, softkick 37.300/37.350 (A600 Kickstart2) and that should fix it. That's what I'd be doing in your situation.