I like the Sharpie idea.
You could also pull down a factory round and then resize it and see if it chambers still afterward.
If you have another shell holder handy might try it.
You could also get after the resized brass vs. the factory brass with a pair of calipers and see if there are any detectable dimensional differences. For starters, how long is this brass that won't chamber?
Have you observed how far the case is actually going into the resizing die as you are performing the resize operation?