Finally, a setup I am familiar with......
I have been running a micro flood and drain system for several years now. I am completely jealous of your tent. I wish I had the space. I have one veg table and one small flowering chamber. Both are micro. The flower chamber is only 1 square foot and is optimized for a single plant. My last recent run produced my personal record of 3.2 ounces of golf ball-sized, dense, rock hard buds. Food for one
Purely from a plumbing and setup standpoint there is nothing simpler. Also, its super cheap to set up, and only requires drilling 2 holes. Once you get it dialed in it is truly a "set it and forget it" method. And one often overlooked plus, it is damn near silent. The good news is that dialing it in isn't that hard. There are only a few dials!
In my experience, the most important dials are flood height, how well your media drains, flood frequency, and flood duration.
Whether your pot sits on the flood table floor or is suspended has not made a difference for me. I often do both at the same time in my veg table. The only time I have found pots sitting directly on the flood table floor to be an issue is when you have standing water in your flood table. That said, a tiny bit of standing water is ok. Most commercial flood trays have small drain channels for the water which often contain a little water after a drain cycle has ended. That little bit of water is ok too......as long as you are flooding frequently enough. More on that later.
All of that said, I think you have already solved your problem by lowering your flood height. Rockwool is a fantastic medium for starting seeds as well as cloning. It can also be challenging sometimes. One of the reasons rockwool and hydroton are so great is that they both hold a ton of water and a ton of air. However, as you have experienced, they both drain at different speeds. This difference is what causes most of the issues I see people new to F&D having.
Soak a cup of rocks with water and let it drain. The rocks will be bone dry on the outside in a couple of days. Fully saturate a 1" rockwool cube, carefully shake off the excess, and the cube will still be soaked 4 days later, maybe more. You need to get the majority of your roots beyond the wet rockwool. You lowered your flood level so that should solve it. If that really was the cause of your problem you should see them pick up in a few days. Once all of your roots are well beyond the rockwool you can lower the water level to just underneath it and let the cube run dry. I would revert back to using your lids with the holes in it. You were right to block the light. A little bit of algae is tolerable but it still needs to be cleaned. Your lid solves that problem completely.
If you get another slow start on your next run, try watering your rockwool manually, from the top, until the roots exit the cube and start licking the rocks. Plants know how to follow the natural, flowing direction of water. I have found that watering from the top, when needed, helps the roots exit the rockwool more quickly when things are off to a slow start.
Here are some additional things that you might want to try on your next run.
Try using even less rockwool. I often cut my 1.5" cubes way, way down to 1/2" cubes. Even a square that small can hold enough air and water to get the seed rolling. Since the cube is so tiny the roots will exit that much quicker. If you germinated your seed using a moist paper towel or some other method it is even possible to skip the rockwool all together and just carefully place the 1"-2" germinated seed directly in a cup of rocks. However, while this can be done successfully, a tiny bit of rockwool does provide better support/scaffolding for the seedling.
Try replacing the rockwool cube with a teeny, tiny cup of perlite. Perlite is also a fantastic medium for starting seeds, cloning, or even running your plant start to finish if your want. I start my seeds in either perlite or a tiny rockwool cube. Perlite, like hydroton, drains super fast. The only problem with perlite is that it is often a nightmare when misused with a flood and drain table. It floats, it can get everywhere, and its just a sticky mess to work with. Tiny perlite is great but it is so tiny that falls right out of a standard 2" net cup. If you take this route you need to line your net cup with something that has smaller-than-perlite sized holes. I run all of my plants from germination to harvest in 2" net cups. There are many ways to create a perlite liner for a net cup. Cut a piece of and old t-shirt to fit, or a coffee filter. If you have access to a k-cup coffee machine it is a little known secret that a k-cup fits perfectly within a 2" net cup. If you cut the bottom off of the k-cup there is even a tiny cloth coffee filter in the bottom! Either cut the plastic bottom off of the k-cup to reveal the cloth filter or don't cut it. If you choose to not cut the bottom off then you will need to poke a ton of tiny holes in the bottom of the k-cup. A soldering iron is perfect for this. The k-cup has a 1-2mm lip/flange on it. If you carefully cut that off with scissors the k-cup with slide to the bottom of the 2" net cup. If you don't, it will sit flush with the k-cup. This mix of 99.9% hydroton and .1% perlite drains instantly and is virtually impossible to overwater. These have worked out really great for me. Peat pellets drain at a wildly different rate than hydroton as well.
Increase your flood frequency. The water flooding over your roots and then immediately draining away is when aeration occurs. If you have media that drains well (not rockwool) you should try flooding more often. I flood once an hour. As soon as I reach my desired height I drain. Also, I know a lot of people advocate not flooding during lights out. I have never tested whether that improves things. I flood every hour 24/7 and have never had a problem. If a DWC plant can sit in warm bath water 24/7 I just assumed I would not harm my plant by flooding every hour. So far, so good.
Sorry for the ramble. I love my F&D and love it when others jump in. I know you will grow to love yours. I don't have all of the answers but I am happy to help a fellow F&D'er if I can.
Let me know if you have any questions and best of luck with your grow!
-Flatbush
