I grow in terrariums and I try to stay away from organic substrates other than the mounted orchids on cork. Whether it's for shelving or otherwise.
To treat your problem I would reccomend that you buy some Physon 20, which you dilute down substanially. Do not use this if you have anything living in the tank other than orchids (reptiles and such). You can treat/spray the diluted mixture and allow it to sit for at least 10 secs. This will rid most of it and prevent most of it as well. If there is not sufficient air movement, though, it will continue regardless. It sounds like you should have plenty.
If you have water standing on the wood that may be the problem. You can coat the wood with sealant or clear coat, or switch to something like eggcrate, which I use. Maintaining a natural tank is much more time demanding and poses more possible problems with fungus, bacteria and pests.
Regarding your gnats. They sound like fungus gnats. Another result of limited air movement with standing water or possibly plants potted too tightly, especially if in sphagnum moss and clay pots.
I grow many cool miniatures. When I pot in clay and use only sphagnum, I have to provide very adequate drainage and loosely pack the moss. Almost all of them want to stay very moist, but not wet. Wet often causes problems. Especially if wet at night.
If the gnat continue, use a small amount of dish soap in a liter of water (a couple of drops works for me). I DO USE THIS WITH MY PLANTS. I spray the tops of the moss, or water it through the mix and allow it to sit. I then flush it out. I will also spray some on a paper towel (more concentrated) to wipe off all the containers and substrates.
***When you flush the pots, if there are remaining fleas or gnats, they will crawl out when the potting medium is submerged. That is when I wipe down the pots with the soapy mix.
These gnats don't harm the plants and are only an irritation.
Hope this helps. Good luck.