After getting my CV64/3D to work last week I decided that I needed to rebuild the system once again so that it was clean.
Egads, man!!! Why would you do this without a backup? It's AmigaOS... No registries or other junk to get garbled up... Pretty much, once you get it working, it usually IS pretty stable and clean, if you were even slightly careful when swapping out files and such...
Anyhow, my guess to get it working again would be to check the monitor config files. ie, make sure you have the right one for your monitor and that it is from the right version of CGx you are running, etc.