I have an issue with some areas on stain absorption in my birch cabinets. We sanded, pre-conditioned and stained the cabinets but now have some odd issues with the way it is setting. Not sure what the problem is.
I'm thinking the wood absorbed water in different areas before the stain was applied? I would try sanding it down, letting it dry for a couple days, and reapplying to see if it helps? Then apply a sealant to the top.
I would seal with shellac or wipe on poly top coat and re-apply stain. Or look into Gel Stain.