Cyano in relatively young systems certainly isn't unusual, in fact its pretty much the norm to be honest. There are allot of theories out there as to what happens and why it may be a short phase or a long one, and why it can come back at later stages.
My own thoughts on this based on what we know for certain tied with a bit of logic is that when you start up a system and add any substrates, you will always get a degree of early precipitation into those substrates (commonly indicated by a short period of Alkalinity suppression commonly tied with Mg depletion) as the sand and surrounding water equalise chemically (look at just about anything you put into seawater and you get some precipitation onto its surface until a chemical balance has been met...)..during this process its highly likely that you will also bind background levels of Po4 into it as well seeing as its pretty inevitable that you will always get a given amount of die off on new live rock when its introduced giving you a pool of free nutrients (even low levels). so in the early stages you basically have a substrate that is pulling nutrients from the surrounding water by diffusion which is then being bound in with any precipitation until a chemical balance has been met...Then over the next few weeks to months you get increasing colonisation of bacteria within those substrates which start to alter what was previously a pretty stable environment, taking up available 02, giving out secretions used to adhere to the surface structure of the grains, and causing a gradual slope of nutrient depletion with increasing depth giving rise to the growth of the anaerobic barrier layer (dependent on grain size and diffusion rate) The more bacteria you get, the greater the difference becomes between the chemistry above the substrate and that within it most crucially pH which starts to fall as you go deeper into the substrate due to oxygen depletion and various secretions from the bacteria present. As pH falls, you start getting dissolution, IE a reversal of the previous scenario where bound Po4 is now being released along with increasing amounts of nitrogen gas as the anaerobic action starts to kick in.
By this stage you've probably had some form of Po4 remover running which has stripped free levels from the main water column above the substrates to below that now found within the substrate layers be that bound or free...all things being equal, the natural pathway for chemistry to equalise across the environment is for some of that Po4 to come out to balance out the situation, and its this initial release of previously bound Po4 combined with various other food sources (nitrogen being another) that triggers and encourages the growth of opportunistic surface dwelling organisms, namely the Cyano bacteria.
As the bacterial population stabilises over time along with the various biological and chemical processes, then the bed settles down to a relatively constant rate of diffusion, and dissolution from the lower (suppressed pH) layers . The Po4 that was previously bound in the early stages during rapid precipitation runs out, and the food supply is cut off. hence why the Cyano disappears after a certain amount of time if the system is otherwise stable and well maintained with a low free nutrient pool.
So what causes later outbreaks ?. Well from my own tests on DSB's and SSB's over the years i would definitely say that in all healthy substrates (IE those that are active both bacterially and well colonised with micro fauna that keep the substrate free and diffusing correctly, that you should end up in a state of constant slow dissolution from below the boundary layer. I've measured pH at various depths in a healthy DSB and found that below just a few inches (sometimes less) the pH can drop well into the region where aragonite sands will start to break down (albeit very slowly) hence the reason that you have to top up sand beds over time as the level falls. (some of it is being washed away into the current and removed as fine aragonite silt via your skimmer, but certainly not all of it) the rest is going into solution....not enough to buffer the systems alk and Ca demands noticeably, but certainly to a very small degree.
In a healthy and stable system, this process should be an ongoing one. what upsets things, is when the water chemistry above the substrates is drastically altered be that by changing salt brands in one go, suddenly shifting temperatures or pH, rapid increases in any element being supplemented, (or nutrients being rapidly stripped for that matter) intermittent top up causing constantly shifting salinity (this is one of the biggest issues)....In fact anything that causes a sudden forced shift in the stability of the substrates chemical makeup.
Remember nature always wants to try to balance things out, the bigger the differences, the greater the effect and longer it takes (in this case I'm talking the differences in elemental chemistry/pH/Temp/overall salinity etc between whats going on above and below the substrates surface (equally this applies to LR as well). If you do something that suddenly shifts pH down or up in the main water column by a greater margin than your normal ambient daily pH range, you have to expect a near equal drop or increase in pH below the boundary layer in any substrates present within a relatively short time frame biologically speaking...what happens then is that you suddenly increase or decrease the rate of dissolution (depending which way you went) beyond what it was previously, and we are back to the same situation we were in a year or so back during those first few months of the systems life with fluctuating rates of diffusion and dissolution through the substrates. and low and behold another Cyano outbreak as the bed effectively 'coughs'...
In the case of ongoing and long term large Cyano populations in systems still exhibiting what would be considered a good low free level of nutrients, then its definitely worth looking at chemical stability, salinity, and temperature stability etc etc...somewhere along the line there will always be an underlying 'trigger' as it were. The Cyano isn't the problem as such, its just an indicator that there is an instability somewhere thats causing a fluctuating environment with unstable nutrient pathways. The Cyano is simply taking care of an excess within its local environment. not necessarily from the main water column.
The annoying thing, is that the presence of Cyano across the substrate actually exasperates the situation. All the time its smothers the sand below, it limits gaseous exchange and diffusion through that sand dropping the pH again which causes further dissolution etc and we end up in a vicious circle despite really good main water column conditions, so syphoning off, is definitely a worthwhile exorcise if we want to stabilise that substrate area quickly.
Just some thoughts.
regards