I know I may be not precise enough, but I haven't used X-Window for few months and I don't know what and how had actually happened. However, I see the result: my xinitrc file was overwrote during some installation. It's a bit of a pain so I have a remark: why don't post-install scripts make a backup, or just ask Overwrite [y/n]?
Regards Krzysztof Duleba