That's odd, it may just be a simple layout problem, because unless there's a bug it shouldn't output any colors that aren't in the palette.
Can you share the palette image? You should be able to upload it here, or you can reach me thru my email (found on my ArtStation), or my Twitter account. Whatever you prefer! If you're comfortable sharing it here though it could be helpful for anyone in the future.
Here is the palette! Thank you for taking a look at this, I tried exporting a few larger sizes too so let me know if you would need thoseHi! I tested this! So firstly make sure you're on the latest version of Pixel8r (2.72). The last one had a bug with palettes.
Secondly, the way I have it interpret palettes isn't very intelligent at the moment. It expects the palette to be laid out as a horizontally laid out, 256 wide image like so:
Testing this one on my end it works perfectly:
That's my fault as I didn't document that well.
A smarter, more unified palette/LUT feature is on the todo list for a future version, though it will be a bit slower to process and probably be part of a big paid update which adds a ton of useful new features (especially for Quake modders!)