I have had this problem for many months. I set up my botnet according to http://www.egghelp.org/enhance.htm and everything works just fine for about 2-4 weeks. Then for no known reason, the hubbot will not ask for opping though the botnet. The bots link up just fine and when you initiate .bottree, they all show up. The only way I seem to fix the problem is by deleting the *.user file and setting up the bots once again. This is a long process to do every month. Is there another way?
What you can do is, you can make your hub bot to share its user file to all your leaf bots. Then what you do in your hub bot (user file) it will be shared automatically.
Could you check the various flags for each bot as it happens. Also, try typing .channel #somechan in one of the leafbots when they won't op the hub, just to verify they recognize it properly.
The long timespan would generally rule out any issues with sharing, such as overwritten userfiles. It would more likely seem like external factors, such as change of ip/dns-names (using dhcp?), or similar