I am currently creating a variable font with 6 masters and 3 axes. When I tested it in Adobe or on the web with only 2 axes active, it works fine. However, when I activate all 3 axes, there is an error where the font becomes larger.
Can you check your master setup? You need to have a master on each axis extreme for each other axis extreme, or, in mathematical terms, a master at each coordinate of the Cartesian tuple of your axis extremes. This equates to 2^n masters required for n axes.
So, for three axes, you need 8 masters. Can you check this?