Here are a few recent published examples in which "your reputation precedes you" is used to allude to something potentially or actually unflattering.
From Jon Land, Kingdom of the Seven (1994):
"Let's say our concerns closely parallel those of the Food and Drug. You opened a door you shouldn't have."
"Bad habit of mine, Maggs."
"Anyone else, we would have ignored it. But your reputation precedes you. Whenever you start asking about something, that something is usually in for trouble."
"And rightfully, in almost every case."
"Not this one," Maggs said flatly, folding his arms before him around his overcoat.
From Mademoiselle: The Magazine for the Smart Young Woman (1999) [snippet]:
Your reputation precedes you—unfortunately. While you prefer to think of yourself as charmingly sociable and experimental, you heartbreakers are often accused of being flighty, flirtatious and kinky (not that there's anything wrong with that).
From Rob Roznowski & Kirk Domer, Collaboration in Theatre: A Practical Guide for Designers and Directors (2009):
Although referrals and securing future work is paramount, one element of the collaboration must be addressed—your reputation. Your reputation precedes you and, in most cases, is never made known to you. It is whispered or e-mailed but rarely shared with you. Your reputation is usually created in moments of highest stress. Review those moments of the production that were most stressful and examine your behavior. Did you "lose it" or did you rationally deak with the problem? Your reputation can usually be traced to those defining moments. Why not change your reputation from someone who "freaks out easily" to someone who is "graceful under pressure"? Reputations can be changed. History cannot.
From Michael Brandman, Robert B. Parker's Killing the Blues (2011):
"I know who you are," Tauber said. "Your reputation precedes you."
"Oh," Jesse said. "What reputation is that?"
"Your serious alcohol-related issues."
From Martha Finney, The Truth About Getting the Best from People (2012):
It's not so easy to fake your reputation. When you screw up in a big way as a manager, word is going to get around. Let's face it. People like to talk. And they especially like to forewarn. So when people say, "Your reputation precedes you," they're not kidding.
From Kelly Edwards, Scorcher (2012):
Aidan suppressed a groan. She was already anxious for the elevator to clear out so she could continue on to her destination.
A name badge caught her eye and she gave him an icy smile.
"That's because your reputation precedes you, Mr. Robertson. Perhaps if you spent as much time on your career as you do chatting up the new girls, you'd have moved up by now."
Clearly, just as reputations can be positive or negative, the implication of the phrase "your reputation precedes you" can be positive or negative.