This happened to my 2000 Jeep Wrangler that I just sold a month ago. My issue was the gear box was starting to leak and needed to be replaced. The funny thing is that if I slowed down my shift, that is I let the shifter rest in neutral a second longer before advancing into 2nd or 3rd gear, I had no grinding sound at all. I would definitely take it somewhere and get it looked at though but you may want to try slowing your shifts a little to see if that will at least eliminate the noise in the meantime.
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