There a ton of things that could potentially cause a problem, and yea, an older version of Apache could be one of them. If the server is the one in your signature, though, that's not likely (that site is running under Apache 1.3.24, which is a couple years old, I think, but not too bad).
Fortunately, we don't have to dig too deeply, because your problem is actually pretty obvious.
Each of the
LogFormat directives in your httpd.conf is defining a different format that is available to you. Those formats are named, specifically
combined, common, referer, and
agent. Your
CustomLog directive tells Apache WHICH of those four to actually use. And, uh, it isn't the one you want.

Change "common" to "combined" in the CustomLog directive and you should be good to go. For one cycle, your log files are going to be mixed with two different formats, which is another way of saying they'll be pretty much useless. You can either wait one cycle before trying to use them or, better yet, investigate how
log_rotate is implemented on your configuration (probably in crontab). Worst case, the next time the system rotates your logs, you'll be where you want to be.