I had a similar problem recently after re-packing my plugins folder. I was using the CPT_No7a_Treecontroller, which wasn't Datpacked, and some of the trees were being replaced with brown boxes. After examining the Plugins_compressed folder, and the Uncompressed plugins, I couldn't find a problem. I deceided to re-pack the Uncompressed plugins, leaving out the Plugins_compressed folder so as everything was re-packed from scratch. I then used the newly packed Plugins_compressed, along with the remainder of my plugins. This seems to have done the trick, and I no longer have any brown boxes! I'm not sure why this happened, but you could try re-packing your plugins from scratch to see if that helps. Don't forget to make backups of the folders before you start, just in case it all goes horribly wrong!
