I have an ethanol plant background so my statement may not apply, please take with a grain of salt:
There were times when our mash would turn a darker color after distillation, and the resulting DDGS and syrup product would be much darker as well. This was due to fermentation not finishing and sending a high sugar load through distillation/evaporation. Is it possible these ferms are not fully finishing and the sugar is caramelizing?
I do not remember there being any off odor when this occurred.
As far as top open/closed: Any chance the yeast are entering the budding phase with the introduction of oxygen? We would use an air sparger to introduce oxygen during yeast propegation, the fermenters were sealed and very quickly turned anaerobic. We typically had little to no ethanol in the yeast prop, we didn't make ethanol until the fermenter. That being said, I can not really believe just opening a top of a vessel compares at all to using an air sparger. Open top fermentation produces ethanol all the time....so I really do not have a good guess...just a wild one.........
Adam