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CSS aggregration breaks site – how to troubleshoot?

I have a number of D7 sites that “broke” recently when I applied 7.39 and a few other updates. By “broke” I mean the site’s CSS styling completely disappeared. I can easily fix by disabling CSS aggregation, so I know that’s the cause.

At first I thought it might be a Omega 3.x problem since all sites initially affected, but then a site based on Bootstrap had the same problem. (The CSS doesn’t always break right away).

What steps can I take to troubleshoot to determine the root cause?

Edit – to add more detail based on Clive’s questions below:

  1. Page source does contain <link>‘s to aggregated CSS files (5 total)
  2. Aggregated CSS files do exist on server
  3. Status codes are 304 (4) and 200 (1)
  4. Folder permissions seem OK
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CSS aggregration breaks site – how to troubleshoot?

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