Not earning shadow pan assault rep
Assuming you are indicting your Pandaren Rogue, my guess is the reputation should be displayed after you have completed Secrets in the Isle of Thunder.
I was earning rep last week from trash in LFR, but this week I didn't earn any rep off trash, only the boss.
That's because you're not neutral anymore. You only earn rep off trash at neutral, once you are at 2999/3000 you can only get rep from boss kills and the weekly quest.
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