Can't say that I've got the problem. Probably the best thing you can do for a recurring problem like this, is to create your own apache install in another directory, like /usr/local
Then, when the next update messes with the default apache install, you can switch your startup item back to your own install, and everything will be peachy keen. I've done my own compiles and installs, but things do occasionally get messed up. Since I installed Complete Apache, Complete PHP, and Complete TomCat, I've had no trouble at all.
See
http://www.aaronfaby.com
Hope this helps.