This kind of error is certainly not related to firmware version.
The EBB does not distinguish between being installed on an AxiDraw, EggBot, or WaterColorBot. The fact that the AxiDraw software recognizes it (and assumes that you have an AxiDraw) does not indicate any kind of problem.
I would recommend that you update the Linux machine to Inkscape 1.0, and use the current version of the AxiDraw/EggBot/WaterColorBot software bundle, available here: https://wiki.evilmadscientist.com/Axidraw_Software_Installation#Linux
Please give that a try, and let me know if you run into any difficulties.