Great, thanks, I will look into xcache.
In the meantime, I think I found the configuration directive to change:
Verification with ctime will avoid problems caused by programs such as svn or rsync by making sure inodes haven't changed since the last stat. APC will normally only check mtime.
This sounds like exactly the issue I've been grappling with. I'll post back once I've had a chance to see how the server response with apc.stat_ctime set to On.