Well that didn't take long, did it? Version 4 of Autozeep adds some more file extensions to the exclusion list.
Additionally, in the previous versions if a file was compressed and was matching the exclusion list, it would not be decompressed (unless it was modified recently). In this version though there is a extra case where excluded compressed files will be decompressed: if their compression doesn't cut more than 5% of their size. This is helpful if you have already compressed a ton of files and then you realized that you shouldn't have compressed some extension. So now you just need to add the extension to the exclusion list and rerun the program. And any files that had that extension and didn't compress well during your previous run, will be decompressed.
Finally, I tested Autozeep on the root of my system drive, not just on my user directory. It worked well. It compressed a bunch of files that couldn't not really be compressed hence the extra extensions that I added to the exclusion list but otherwise it worked just fine. Now I just need to let my defragmenter do its thing. I am using Diskeeper 16 by the way, it's good, I may write something about it in the future.
You can download Autozeep v4 from here.
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