I think the problem may be with the way routers2 handles caching.
Here, I use speedycgi, which will cause a processing thread to respawn after a certain time or number of iterations (meaning that it respawns overnight, when the new archives are created). mod_perl, however, NEVER respawns until Apache restarts. This means that if the cache gets out of synch it never notices.
Now, there are a number of age tests to make sure .cfg files get reloaded if they change (which fixes the problem for mod_perl), but I don't have this set up for the routers2.conf caching, nor for the archive-dates caching, and so it appears that mod_perl people will add new archves but routers2 doesnt notice them until Apache is restarted. Similarly, changes to routers2.conf will probably not be noticed until Apache is restarted.
This is clearly a bug... err, I mean, a 'feature'

. So, in v2.18, I will add some extra checks to invalidate the cache of routers2.cgi if the file is changed since the last read, and also to invalidate the archive dates cache is the archive directory has a modify time since the last read, which should solve the issue.
In the meantime, I can only suggest one of
1) disable caching in routers2.conf. This will slow things down, especially if you have a lot of .cfg files
2) restart Apache (hence reinitialising the routers2 mod_perl threads) every night - maybe not practical
3) switch to speedycgi (unix only)
If this is causing major issues then please keep bugging me and I'll send you a beta with the fix. I'm off on holiday tomorrow for 5 weeks, though, so things will be held up until then.
Thanks for helping to track this one down, its a complex set of circumstances needed to trigger it which is why it avoided the testing.