There are associated costs to running and owning any corporation. Granted the costs aren't always written down in understandable terms. But they are pretty steady and do not fluctuate greatly from month to month unless something is going on, )ie: supplies, change in taxes, a slew of other things)
Please be more specific with your problem. I'm having a hard time trying to figure out your exact problem here. As far as I can figure, you are wondering why their is the occasional decrease in quality and efficiency upgrades? If so, I believe the game takes into count periodic deterioration of product supplies and facilities that require maintenance. Supply quality is ongoing and is geared toward buying you the quality of supply you ask for. Sometimes if there isn't enough product that you require being supplied your product quality will decline because it doesn't have that same quality being supplied to that corp anymore, that is until you start getting the supply problem alleviated. If you manually supply a corp with product from your own country, it will give it the average quality rating that your country had in stock, not necessarily the best quality you had, which in turn will reduce the quality of good being produced. It is temporary and works itself out when your ordering supply strategy problem is no longer a problem.
I hope this helps. If not be a tad bit more specific and I will see what I can do.
T.