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I've inherited a website whose permalinks are 200 and open fine:

http://www.example.com/test-1

While looking at the source, the shortlink specified in the link tag points to 404s:

<link rel='shortlink' href='http://www.example.com/?p=6' />

I'm unsure of what the source of the problem may be. I've noticed that Jetpack had been enabled before, but is now deactivated. I can't say for sure it's one of the plugins.

The following is a list of enabled plugins:

  • !Share
  • BackupBuddy
  • Contact Form 7
  • Facebook Social Plugin Widgets
  • Gravity Forms
  • NextGEN Gallery
  • Pinterest "Pin It" Button Lite
  • Platinum SEO Pack
  • Really Simple CAPTCHA
  • Referrer info for Gravity Forms
  • Slimbox
  • WordPress Mobile Pack
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Deactivate the plugins one-by-one to isolate where the problem is coming from. It looks like your shortlinks are not working at all. –  vancoder Jun 26 at 20:38
1  
Seems it was one of the plugins, WordPress Mobile Pack, causing the shortlink to point to a 404. Thanks Vancoder. –  ghdiep Jun 27 at 20:53

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