John,
Anything you do to process images in the linear stage requires a very delicate hand and, unless you have great SNR, can do exactly what you are seeing. The problem is that you end up creating a mess in the linear stage that gets exaggerated when you do your stretch. In the first instance, you should never run Atrous or MMT in the linear phase and, depending on your data, even go easy with MLT. Given good SNR you can also apply a little TGVD in the linear phase, but even with good data that can be tricky. Given what you are seeing, I would strongly recommend doing only minimum processing in the linear stage beyond maybe DBE and background neutralization and color correction. Save everything else until after you stretch the data. You can then clean up your noise with TGVD. The key is that what looks like very minor variations in the linear phase get stretched to a mottled mess when you go non-linear.
If possible, try sending a link to the image that comes out of BPP, but before you do anything else so we can see and play with the data.
For what it's worth,
Best,
Jim