Ok, so I had the theory that the crond script was not running properly, or stopping or starting, but I don't think this is the case.
Some of my clients nextduedate entries in the tblhosting files are now set to December. They have skipped November. I noticed this before any invoices have been generated, so it is not the actual invoice generation code that does it. The dates are getting pushed in the future somehow by some other process.
This problem is notorious to debug. I've since noticed 1 more account that had the issue, and I am going to keep a watch for them when they are to have their next invoice generated. Maybe I can figure out some commonality between the accounts that have the problem.
Have you had any luck?