May I know where you define the dimensions? are they inside a structure group or inside "model"? please check geometry and compare the dimension. I have not seen any report that the simulated dimension is such different from the original setting. The only reason I know of is, the actual dimension is set somewhere through a group.
You can do a simple test with a rectagle waveguide only and make sure the dimension does not change. Or you can copy the correct geometry with material to a new project file, which will get rid of "model" control. You can also post some geometry settings here.
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