It' not related to SimVim interface. The slave board simply receives data and work as a driver, translating it into stepper positions. The stepper smooth motion processing and speed depends on the frame rate and value of the data changed.
As the latest versions of Air Manager have included their own interface for Arduino with serial connection, it's possible that it's sending something to the serial port that interferes with the stepper board, if you're using a USB cable from the computer to power it.
Try disabling Air Manager's serial capabilities, if it's possible, or power your slave board from a wall adapter, not USB.
Another option could be the drop in X-Plane frame rate when using Air Manager (how much does the frame rate drop when you launch it?), especially if you use additional monitor connected to the same computer, the frame rate can fall drastically depending on your video adapter performance capability.