I'm having the same problem I've been asking around and Koush told me to just keep the bootstrap recovery installed after u unroot, I did that and my phone boots up like normal but its still running off the recovery. From what I understand you have to go to terminal emulator and input a command to get it completely off. Here's what (RoOoLeR ) over at Droid X forums emailed me I haven't tried it yet so let me know if it works out for you. Also check out his rooting guide it helped me with alot of stuff

To remove Clockwork is very easy dont worry

to remove it.. download Android terminal from the market and type the following in.. this information was pasted out of my guide. ->To Remove Clockworkmod<--su -mount -o rw,remount -t ext3 /dev/block/mmcblk1p21 / system -rm /system/bin/logwrapper -rm /system/bin/hijack -cp /system/bin/logwrapper.bin /system/bin/logwrapper -mount -o ro,remount -t ext3 /dev/block/mmcblk1p21 / system -reboot let me know if that helps. Karston Davis (RoOoLeR)