Chad,

I have cleaned them, and I also have lived in a log home for the last 12 years. I clean mine every two years. We pre-wet, use a 1/2% solution and start from the bottom up, to avoid streaking. Then rinse and rinse again. I use an oil based stain on my house called WoodGuard, specifically designed for Log Homes. It really doesn't get blotchy, but I am sure it could if the stain is a dark color. All of the ones I have cleaned have been a light color, like Golden Oak/Cedar. When it comes to a water based stain that does not sink in, I would think it might get a little blotchy depending in the amount of stain still on the surface, that has not weathered off. 

Hope this helps...