There are several different things that can cause drastic PH increases.
1) Biological action. It could be from algae, or other bacterial growths in your rez, or in your case, also in the buckets. As far as I know the only solution for this is to use IN-organic nutes with absolutely NO ingredients derived from anything organic or plant based. Something like Jacks 321 hydro will work great, but be careful if you use any cal/mag, or other additives that have ANYTHING derived from plant material.
I had this exact problem when I was using Advanced Nutes PH perfect line, Mega Crop, and Fox Farm nutes. Once I switched to Jacks321, that all went away and I was able to reduce the chlorine I add to next to nothing. My rez stays fresh for up to 9 days between refills. I am drain to waste in an AAA setup, so no root exudates to worry about.
2) It could also be from the roots interacting with the solution, but that is dependent on your EC level to some degree, but if you have bad bacterial growths, your screwed. This is less likely in your case because your roots are still small.
Bottom line - do not ever use anything organic in hydro.
3) The calcium/alkalinity of your water is the next one. Every time you PH down, the dissolved C02 level increases, which lowers the PH by the formation of carbonic acid. Unfortunately, when you aerate, the excess C02 in the water leaves the solution, which lowers the concentration of carbonic acid, which raises the PH. The more you aerate, the faster the PH goes up. The worse your calcium problem is, the higher it will go. Basically, your water has what I think of as a 'natural' or preferred PH level once every thing equalizes - dissolved C02 mainly. When you PH down, then aerate, it wants to go back to that PH. How bad this is depends on your water, but if its well water, there is an excellent chance you have this problem to some degree.
4) The other thing is temperature. I just confirmed this recently in my grow. I try to keep my rez water around 65F as a max, but that water feeds down to a small holding tank that is about 1 liter. That small tank is used to adjust the water level for the AAA nozzles to siphon from, so it has to be near the root chamber. That area where the tank sits varies from the hi 70's to the hi 80's temperature wise because I have to heat my root chamber or it stays too cold. So that water in the tank varies from the upper 70's to mid 80's, while my rez stays at no more than 65F and often down to 55F when I do a rez refill or add ice to keep it cool.
Here is where the problem arises. The dissolved C02 level goes DOWN when temperature increases, and goes UP when temperature decreases.
Remember the dissolved C02 forms carbonic acid which is what lowers the PH. So, any time there is a temperature change, the carbinic acid level changes which changes your PH. In my case, when the rez temp is near 65F and the siphon tank is down near 75 F, the PH goes up by about 0.1. When the rez is cold at 55F and the siphon tank is at 85F, the PH difference will be 0.3 to 0.4. So when I was setting my rez to 5.8, my roots were being sprayed at 5.9 to 6.2 PH.
YKeeping your water temps higher means your PH will want to stay higher. Keeping your rwater temps lower means your PH will want to stay lower.
I have been fighting all these issues for two years trying to sort out why my PH was impossible to control. It turns out I have all of them. My solutions were as follows.
1) Never ever ever ever ever use anything organic in the rez - ever. Bacteria and algae just love that crap and they grow like mad when its available. By the way - this very much includes any so called "beneficial bacteria". Dont use it. I also am absolutely fanatical about light discipline as far as light getting into the rez, any fitting, and all tubing. Algae wont grow if there is zero light, but you must check all fittings, and pipes, buckets, lids etc.
2) I dont have to worry about my roots messing up the PH because they never touch the rez water or the siphon tank water. Once the roots get sprayed, the runnoff get tossed out. I am drain to waste. In your case, as long as the EC is close, that should be easily manageable.
3)My alkalinity/calcium problem isnt too extreme, but it is there. My water likes to be at around 6.4-6.5 PH. I handle that by doing the minimum amount of aeration I can get by with in the rez. Plus, I keep the rez remps low - below 65. I use an aquarium pump in my rez to keep it stirred up and it flumes the water surface. It also has an air line that sucks in air and puts out small bubbles when the pump runs. I only run the pump 1 minute out of every 15. Just enough to be sure no anerobic bacteria can get started. I get all the aeration I need by the air atomization from the spray nozzles, and the micron sized droplets. You wont want to keep your water as cold as I do - your roots wont like it. 68-70 is probably the ideal range for your situation.
Hope that helps, and good luck!!!
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