Using include file and include virtual is failing at a very low rate. Less than 1% in my roughly 1,000 page loads worth of testing. When this occurs the files are not included and there are no errors reported in the logs.
Seems random at this point. Just reloaded a page with the includes several hundred times and eventually it will happen. Sometimes in the first 50 loads, sometimes 300. Wouldn't have noticed if a client hadn't pointed it out.
I've created a script to do the testing in larger quantities and so far the results indicate that this problem does not occur with include virtual. This is only an issue when using include file. It also seems to occur in intervals. Every now and then it will occur just once but often repeated requests will fail for 2-10+ seconds. My testing interval was half a second.