Aperture black and white filters making images blotchy

Hello All!
I'm having some odd issues with Aperture and using the black and white filters: mainly red and orange filters. I have tested this with different cameras (all raw) including Nikon D700, Olympus E-M5, Canon 5D mk3, Nikon D800; all exibit the same issue. I have also had a friend test this on Lightroom and the problem did not appear.
Picture a landscape with a blue sky. Upon adding a red filter, and sometimes orange, the dramatic dark sky one would expect with such filters becomes blotchy. It looks somewhat like bad JPEG compression or noise from high ISO images but these pictures are all generally ISO 100 or 200. Sadly, this prevents me from printing these images so I've had to find other ways of processing them. Even when exported as a 16-bit TIFF, the problem persists.
Anyone have any thoughts? Experienced this themselves? Thanks for any thoughts!

Thanks Kirby... I have checked the channels but perhaps there is something I'm missing. Here is a screenshot of a random image I have but it shows the issue well. These are at 100%, ISO 200, red, orange, no filter (respectively). The histogram is from the original. No other post processing done. The red is the worst offender... the orange isn't as bad but it can be worse on certain images.

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