I'm having some trouble with the contention that this is just such a rare thing. I do a lot of audio signal processing so I'm used to dealing with noisy signals at Khz rates. Threshold fluctiations are a fact of life if you're trying to do things like pitch detection, envelope following, or sidechain compression (all of which have obvious analogs in the trading context).

Obviously you don't want to impose too brutal of a low-pass filter on your input because you would miss important signals, but what prevents you from running the input signal to an LPF in parallel and keying a noise gate when the amplitude of the low-frequency (trend) signal drops? This is such a common problem in dealing with audio that we use specific devices called de-essers for recording vocals, because sibilant sounds otherwise tend to throw off other components of the signal chain: http://en.wikipedia.org/wiki/De-esser

Ironically, you mention using XKCD-type graphs because 'nobody reads' the explanations and caveats, but just looks at pictures. I wonder if you aren't missing a trick here by over-engineering your HFT systems for speedy response at the inevitable price of positional confusion. Is it possible that you're using Infinite Impulse Response filtering and running into denormalization problems as a result? If so, can you not rectify the problem by adding a small amount of noise?

I get your point about the negative aspects (for the HFT trader) of quote stuffing, how it can easily lead to being on the wrong side of a trade or punishment by the broker for flooding the output channel with unintended orders. But, you want to make money from automated signal analysis, that's your problem in much the same way that a sound engineer is responsible for preventing transient pops and feedback howls in an audio network. Sure, these problematic signal conditions are statistically rare, but when you're dealing with a high volume of samples you'r going to run into statistically rare conditions on a regular basis - and indeed you mention that this is the sort thing you might expect to happen once a day.