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I'm trying to take samples from my Alesis Wedge reverb unit.  One program that simulates early room reflections is particularly troubling, as every time I deconvolve it using various settings and different lengths / sample rates of test tone, I always end up with an impulse that has the sine sweep present in it.  I didn't have this issue with most of my other outboard reverbs as of yet, and the program in the Wedge is listed as an "ambience", which seems like something that shouldn't be too difficult to capture.  Are there any obvious reasons you'd still hear a sine sweep in your deconvolved impulse?

This problem is known: the fact you get a trace of the original sine sweep in the deconvolved impulse file tells that the device (in its particular mode of operation) you are recording has some sort of non-linear behavior - it may have harmonic distortion or chorus/phaser like behavior happening.  This situation cannot be resolved by any means, because Deconvolver can only produce impulse responses of linear time-invariant (LTI) devices (rooms).