I am speaking as a recording engineer. I am somewhat specialised in acoustic music. Myself and several of my associates have noticed problems with Elixir and all the other coated strings.
When it comes to mix time, there is a real stuggle to achieve a sound. Often one ends up with compromise. One has to try to remove the Elixir quack with eq but not castrate the instrument. It doesn't work. My guess is that the higher harmonics go increasing out of tune with coated strings. Like bells and tuned percussion. After all it is no longer a rod of steel, but one sheathed in a Teflon tube! i.e. non-homogenous material, likely to have a non linear response. One of my associates, an engineer and a fine guitar player, refuses to record these strings, due to the certainty of problems later. I am there also.
Best Regards, DD Sound Sound - Homepage