What are the requirements for a stable carbon cycle in sealed "bottle gardens"`?
The problem lies in soil bacteria. 
There has been a project on a larger scale: Biosphere 2. After their initial trial they realised $O_2$ levels are getting much lower from what was predicted. The scientists team investigated the problem deeper and came to the conclusion that there was a lot of dead organic matter in the soil, which got consumed by aerobic bacteria. There were also other hypotheses: not enough sunlight and $O_2$ sequestration by concrete. 

A solution for you would be to make sure there is little organic matter in your soil. Perhaps use inorganic "soil" like sand + some nutrients. And also make sure there is enough sunlight.
Start also with small plants - too large plants in the beginning might change $O_2/CO_2$ ratio to abruptly during day and night cycle. (remember that plants are also consuming oxygen at night).