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Most probably amcl is right and you are computing your values incorrectly.

As the transforms you get (i.e. odom->base as well as map->odom) are not in the same frame, you cannot just add up the single components. The frames (in this case, odom with respect to map) is rotated. So you have to adjust the x and y components according to the orientation. I'll leave it up to you to verify this is correct. Check how to transform coordinate systems.

If you want to get the transform from map to base in ROS, you can directly ask tf to get you this instead of manually adding up the transforms.