Metformin can cause some unpleasant gastric side effects in some people which is why they advise taking it with food. If you tolerate it well and there is no adverse reaction to taking it on a empty stomach then you don't have a problem. If you don't eat any breakfast it's quite natural for your liver to help out by releasing some stored glucose. Personally I look on this as a positive, getting it out of my liver into my blood where it can be used.
If you would rather not see your levels rise maybe try some cream in a coffee, the cream should fool your liver and prevent it from dumping glucose