NAIP images are four channel images. If you shuffle channels so that the R, G and B display is driven by what used to be channels 3,0,1, that still leaves the fourth channel (Channel 3) as it was originally.
When you export the resulting four channel image to a TIFF, how viewing software displays that fourth channel is up to the software.
By default, viewing software like Photos in Windows 10 treats the fourth channel as an alpha channel, so where Channel 3 has high values the transparency of the image is high. In some viewing software the "background" is assumed white, so as more of that shows through the image is lighter in those places.
In PhotoShop, high transparency (high values of the fourth, alpha channel) results in more of the default checkerboard background pattern showing through.
You can see the effect by opening your Flying L Ranch image in Manifold and then in the Style pane using the Channel quick select button to choose RGBA. It will then interpret the fourth channel, Channel 3, as alpha, and you'll see a similar effect to what your image viewing software shows.
The solution is to either a) before export set all values in the fourth channel to 0 so the alpha channel says "make everything Opaque" or b) create an RGB three channel image from your RGBa four channel image and export the three channel image.
Option b) is easy to do using the Join dialog: Suppose your four channel image is called "Ranch":
1. Open Ranch and in the Transform pane use the Channel template to save Channel 0 to an image called Ranch RGB. Ranch RGB is a single channel image with one channel, Channel 0, taken from Ranch.
2. Create a map with both Ranch and Ranch RGB in it.
3. With the focus on Ranch RGB, launch Edit - Join and choose Ranch as the joined image.
4. Click the Add button, then Fields.
5. Choose Channel 1 and Channel 2 to add
6. Press Join Component. You've now added two more channels, Channel 1 and 2, to Ranch RGB to make it a three channel, RGB image.
7. Click on a different layer and then back onto Ranch RGB to refresh all the styles, and then in the Style dialog in the quick selector button choose RGB as the layout for channels. You now have a normal looking RGB image that only has three channels in it. Export Ranch RGB and there won't be any fourth channel for software to figure out.
You could, of course, use SQL to modify the fourth channel or to drop it, but the above is just point and click all the way. Transform templates for images really should be enhanced slightly so that instead of there being just a limited selection for multi-channel images, that all the many templates that work with single channel images would appear but with a channel selector control so you could apply what they do to just one channel in a multichannel image.