You only get the alert once; until you go back and read the thread to its end again.
This can make it
appear as if you are not being alerted, when what's actually happened is you've (accidentally) overlooked the alert. Happens to me all the time when I'm rushing in / out.
The way to confirm this is by looking at ALL of your recent alerts and searching for a thread you're
expecting to be alerted about:
http://www.cyclechat.net/account/alerts
Let me know if you find any of the "missing" threads amongst your list of alerts?
Cheers,
Shaun