By background, I run a set of National Language (NL) forums over a shared phpBB installation. Basically each forum is a skeleton directory with symlinks back to a shared coded base (exept for cache, files etc.). See http://wiki.services.openoffice.org/wiki/User:TerryE/phpBB3.0.4_Migration_%E2%80%94_Detailed_Implementation_Notes#Standard_NL_configuration if you want more info.

Everything worked fine apart from the cron functions. After quite a lot of debugging I eventual found the problem in that common.php includes at lines 117-120 the following:
if (defined('IN_CRON'))

I am lost as to the reasoning behind this since cron works fine without it and in my case just works. Given that you are planning to rework this for 3.2, and the logic for this is probably redundant now, I just wanted to suggest dropping this redundant exception.