Earth's history: The Great Oxidation Event and the 'Boring Billion'
Your question probably arises from a misunderstanding regarding the 'flooding' metaphor. I would not assume that 'flooded Earth's atmosphere with oxygen' means a lot of oxygen in the first place ... the metaphor means that oxygen levels rose from basically absent to noticeable.

If you look at the history of oxygen in Earth's atmosphere you see a general trend of gradual increase with a 1GY lasting stationary phase (Holland (2006), picture taken from above linked Wikipedia article - red and green lines are upper and lower estimates, respectively):



After initial atmospheric oxygenation about 2.5 GYa, Earth's oxygen sinks (mainly the oceans, after that landmasses and the ozone layer) were filled and buffered atmospheric oxygen levels, keeping them low. Once those sinks were saturated (approx. 850 MYa), the atmosphere started to oxygenise rapidly.

The constant (or as discussed below: drop in) oxygen concentration is caused by these sinks. The oxygen that is produced by photosynthesis was just not available to Earth's organisms as it was not atmospheric. 

As @GerardoFurtado points out in the comment, modalities of the stationary phase are still debated. A review by Lyons et al. (2014) presents evidence that after the initial increase in oxygen levels, a drop in atmospheric oxygen preceded the stationary phase (see their Fig. 1, blue boxes). This does not change much as the newly inferred stationary phase, though probably a more fluctuating stationary phase than suggested by Holland (2006), is still higher than before the great oxidation event and lower than at present.

The major conclusions remains the same: There is evidence that the seemingly slow evolution 2-1 GYa was probably caused by oxygen limitation and oxygen levels were buffered by oxygen sinks. The change of oxygen concentration was determined by both the rate of oxygen production and the rate with which oxygen is stored in those sinks; the interplay of those rates caused the oxygen concentration to remain constant, drop or occasionally even rise, i.e. fluctuated.