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Is this some sort of non-profit organization that is paying it?

A pension is ordinary income, but reported on a 1099-R.

A 1099-MISC box 3 is not subject to SE tax, only box 7 income is.

@dmertz have you come across a pension on a 1099-MISC before?  - Does not seem right.
**Disclaimer: This post is for discussion purposes only and is NOT tax advice. The author takes no responsibility for the accuracy of any information in this post.**