After my overnight security report audit came in, I noticed that Apache needed to be upgraded. I went to FreshPorts to see if a fix had been committed. While there, I noticed a lack of vuxml skulls against the latest versions of Apache. Checking the BETA website, I saw it was correctly marked. More digging found the problem. In the process, I improved some error reporting in the scripts so that this problem should be brought to my attention much sooner.
Things should be back to normal now.