Rice left in water for several months - what biological reactions or growths would occur?
It is likely a volatile organic compound (VOC) that is released as a by-product of microbial metabolism, although microbes can also produce some inorganic compounds, such as hydrogen sulfide (rotten egg smell). It could be any of a number of compounds, depending on the microbial species and the environmental conditions. The only relevant paper I could find based on a cursory search was by Yanqiang et al. (2013) on volatile compounds released from the anaerobic digestion of food waste in general; based on the results, the odor likely consists of a complex mixture of gases, and may be especially rich in aromatic compounds. Whether it could have any negative health effects is challenging to prove, but you would likely want to avoid exposure.

I presume that your container is made of plastic or at least contains a silicone ring. You can remove odors from metal or glass by washing them, but porous substances like plastics, rubber and the like will absorb volatile compounds, rendering them largely inaccessible to solvents such as water, and will release them slowly over time, which you can perceive via olfaction as you have noticed. If you want to eliminate the odor faster, you will need to accelerate this outgassing process. The way this is usually done is by baking in an oven (optimally in a vacuum, although this is not necessary). The rate of outgassing grows exponentially with the temperature, so you should use the maximum temperature that the material in question can withstand.