In a previous post, I noted this issue in for project icons:
I have the same issue. It seems to be when a .png is attached to a thought type, it no longer displays on the thoughts assigned to that type. However, if the thought type is assigned an icon through copy-paste, it works correctly.

There is a workaround. Edit the thought type and choose [Open Folder for this thought]. Then rename the .png file to TheBrainIcon.png. This will resolve the issue.
Windows 7
OSX 10.6.3
Java SE 6

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