After playing around a bit, I found a workaround. The problem is that after a reset, the home screens are drawn, but PNG's on SD are not ready yet, thus the generic icons in the folders.
By moving just one app from SD back to phone (preferably something small), the home screens are redrawn (you see a white screen with "htc" for a few seconds), and all missing icons return to normal.
Another workaround is to change your skin and then back again. This may be more of a hassle if you have a custom wallpaper, though, since you'd have to change back to that as well.
The trick using the method of moving an app back to phone and back may be quicker/easier.
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