been there done that. I never use the feed rate change. I edit the g code instead, which can be a hassle if there are many feed rate changes. Might have to go back to the cam software and re-do your toolpath from scratch. This is one of many problems when you make one offs. In production, the first piece is sacrificial while you optimize the code.
Now you know the software has a quirk, you can work around it. Use nc verification software or backplot your toolpaths as a matter of procedure.
You know that problem you have where the thing goes wrong and everything gets screwed up? Stop doing that.