We have a known issue where site e-mails are only sent from about 1:30 am (eastern) until mid to late afternoon. This includes both private messages and subscription notices. Daily notices (for threads or subforums) are supposed to be sent at 1:00 or so, and therefore don't get through. Instant (for threads or PMs) can happen at any time, so if its in the morning you'll probably get it. In the evening, probably not.
Other members have made threads about it, but I'm not surprised you didn't find them. There are a bunch of issues that have the same root cause, and different threads have come up with very different titles.
http://www.camaro6.com/forums/showthread.php?t=409324
http://www.camaro6.com/forums/showthread.php?t=435798
I hate to say it, but currently there is no fix. The best I can offer is what I've ended up doing. I have set all my subscriptions to 'weekly', for both individual threads and for subforums. The notices come in at about 1:30 am Sunday night (Monday morning). I also use the UserCP to check on my subscribed threads on a more frequent basis. I don't like it as much as how I used to be able to do things, but its the best I can think of for now.