This is a bug that was initially reported for Experimental 8.0 and 8.1 (see here (http://forum.simutrans.com/index.php?topic=5296.0)), but I have reproduced it using the latest Standard nightly build. From my preliminary investigations, the problem appears to originate in fabrik_t::step(long delta_t), where the variable delta_menge has a non-zero value even when the factory is not producing. I have not yet been able to track down the ultimate origin of this bug. I am wondering whether it might relate to another mysterious industry-related bug so far reported only in Experimental, but that is very hard to reproduce as it is entirely idiosyncratic: details here (http://forum.simutrans.com/index.php?topic=4716.0).
A factroy produces, as long as the storage is completely filled. When the production reached one unit, there is a chance to spawn a field (or emit smoke). Thus initiall factories could still very slowly produce until saturated. Currently factories start with 16 units before filled. I change this to completely filled, which should take care of this problem.