I’m not certain that I fully understand the issue that you’re describing, but I suspect that it’s one of these three. If it *isn’t*, please say so, and help me understand exactly what the situation is.
(1) In Inkscape’s Preferences, under the “Interface” heading, there’s an option: “Origin at upper left with y-axis pointing down”. If you check that (and restart Inkscape), the (0,0) corner of your document will be located in the upper-left corner of the page on your screen. This *only* changes the labeling of the on-screen coordinates and rulers; it does not affect the document or how it prints. However, it may help you to visualize the plot if the coordinates look reasonable to you.
(2) You may be seeing the normal results of “auto-rotation”: see section 6.3 “Document orientation” in the AxiDraw user guide. Documents that are taller than they are wide are normally rotated, 90 degrees counterclockwise, when they are plotted, to reconcile the wider-than-tall plot area with portrait-mode artwork. You may prefer to disable this behavior and work only in landscape mode (or otherwise model the full plot area of the machine in your document).
(3) You may be expecting auto-rotation, but in the other direction. If you’re expecting clockwise rotation but seeing counterclockwise, then it will feel like there’s an extra 180 degree rotation in there. There’s a hidden option in the axidraw_conf.py configuration file that you can use to rotate the other way: set
False. This file can be found in the Inkscape User Extensions folder — with the location visible in the Inkscape Preferences System heading. In the CLI, you can use a copy of this file with the
--config option to specify that (and your other defaults).
Finally, you might want to consider using Preview mode, with rendering enabled: It will show you the plan for how the machine will plot a given file, including how it travels from and to the home corner at the beginning and end of the plot. In many cases, this can help to resolve any ambiguities that you’re seeing. Preview mode is available both in Inkscape and the CLI.