Tedc Like snake and others I am going through something like this. Its funny because when my mag dropped to 950-1000 my sps where doing ok."not growing but not dieing" now over the course of a couple months bringing my mag back up "which i was hoping would help stabilize my alk" I have sps dieing from the bottom up. If you idea of an imbalance of bacteria is true then wouldnt dosing carbon fix that? If some how bacteria is using alk as food then giving it a different food source fix the alk issue.
Yes - but it's a cure I never recommend. your fixing issues in the short term by carbon dosing but the underlying problem continues. now your stuck carbon dosing and over-skimming to catch all the extra bacteria. Sure, it fixes your one issue of freeing up the locked up carbonate used by the bacteria - but what caused the imbalance in the first place needs solved.
I also don't know of a natural mechanism in a real reef that equates to carbon dosing.
Honestly, the more I think about this - Roger may be onto something with "seasonal affective disorder" in corals related to the switch between chloramines and chloride disinfectants (sorry - seasonal affective disorder will be well known by northerners - its sort of a joke).
Maybe those of us that make our own water through our own RO/DI units (and have tanks less than 300 gallons to dilute incoming water) are more susceptible to the trace ions coming through or getting past our DI resin. Like roger said though - there's no data whatsoever on real time water testing and what the water companies are sending us during this switch from chloramines to chlorine back to chloramines. The problem seems to occur just before the water is switched to chlorines or during the chlorine treatment. thats just too weird and coincidental.
I have no scientific explanation for it either - since ro/di units are supposed to be better at chlorines than chloramine. Maybe the extra chlorine is breaking things off the carbon blocks that are normally locked up when treating chloramine water?
Scientifically - I think I can come up with a scenario:
Let's say it's ammonia getting broken off the carbon block during this chlorine purge the water company does - it gets through your ro membrane - some of it (less than 1 PPM) gets through your DI resin. you could be dealing with 0.25 PPM ammonia in your saltwater mixing station and not know it. Your TDS reading on your RO/DI would still be zero.
OK - so you've got extra ammonia going into your aquarium - more than is normally produced by the fish and other livestock. It's not alot. it's not killing the fish. Its only an additional 0.25 PPM.
What happens next? Well, you've got extra nutrients that the bacteria love to consume. They are happy and they start "getting it on" and reproducing. Now you've got the imbalance of nitrifying bacteria to denitrifying bacteria (which probably take around 6 weeks to catch up). you may be in fact running a mini-cycle. The only way to tell is if you see a rise in your nitrates. The increase in nitrifying bacteria means a decrease in the available alkalinity. The decrease in alkalinity may stress corals (or some other mechanism may be at fault).
In Snake's case - if his rock is clogged with detritus and mulm - then the denitrifying bacteria can't re-populate inside the rock cause it's plugged up. the only place they may be is in the sand (if it's deep) in his display and maybe in the refugium. Properly designed refugiums are only taking on around 10% of total system flow through - so it's going to take longer for the nitrates to make their way to the refugium.
So here's a question or two for snake to see if the theory holds:
Do you make water as you need it for a water change?
Do you have a holding vat for RO/DI output?
Do you buy your water from an LFS?
My thinking is: if you make 10 gallons at a time for a water change and use all of that 10 gallons directly - then you may be experiencing the above.
If however you have a salt water mixing station and your holding take is 100+ gallons - then the water you may make during the cross-over may not have an issue - as it can be properly diluted with the holding tank water (and/or have an opportunity to off-gas).
If you buy your water from an LFS - I think most of them have holding tanks greater than 100 gallons - so they are also unaffected by the cross-over.