Mike,
Looking at your pictures the sole looks like it has been in a bad fight. Wonder what the other guy looks like

.
Nice boots. First thing coming to mind on the sole is the stain being absorbed unevenly. That will happen if the grain is taken off in an uneven way. Still those spots are quite dark. Have you tried a piece of scrap leather and finish it. See if it's something in the leather (not likely) or something that happens to the sole after you put it on and before you finish it.
Sorry I can't be of more assistance. It could be something obvious you do but I'm not picking up on it.
When I scrape I hold the glass in one hand, not both hands as in your picture so I don't press too hard. As Mack suggested, feel the glass do it's work, don't go to deep. The purpose is to just take the top of the grain off, not to dig down to the flesh side

. You probably have to re-break your glass to do a full sole, once piece will get to dull.
Maybe this image helps.
6912.gif
Leather is a preserved skin. The black line under the new skin layer on the image will be the grain of the leather once tanned. The remaining epidermis and most of the dermis is your leather. The subcutaneous layer is discarded by the tannery and made into Jello. When you scrape you do not want to go through the epidermis layer. The image is not to scale and the epidermis is not very thick.
Rob
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