I've just submitted a bug (3889) about destroyed MBR and Dustin Navea asked me to subscribe to this list. Here comes some detailed description:
As a regular user I've launched winecfg as a regular user, then proceeded to the dist setup. I've tried several options like automatic configuration, manual configuration. Then I've tried to change some drive letters manually. After reboot a "PRESS A KEY TO REBOOT" message appeared instead of a GRUB screen. Next time I booted with grub-floppy and then restored the MBR with grub-install /dev/hda. Please let me know what additional information you need. It's happend on Slackware 10.2 system, 2.6.14 kernel with ck-3 patches.