When two nodes in the central area are aligned horizontally, the height of the graphic changes after clicking the "select and transform objects" button

(i) I have a graphic with W = 537.042 and H = 537.042. It has 335 nodes. The nodes at the bottom have Y = 370.532, and the nodes at the top have Y = 907.565
(ii) There's a pair of nodes at (101.405, 705.171) and (638.446, 705.165) that I select and align horizontally
(iii) The Y co-ordinates of the nodes at the top and the bottom of the graphic do not change
(iv) I press the "select and transform objects" button with the graphic selected. I find the height of the graphic has changed from 537.042 to 537.043
(v) When I then press the "Edit paths by node" button and check the Y co-ordinates of the nodes at the top and the bottom, I find they have changed (to 907.567 and 370.534 respectively).

In short after the hoirzontal alignment, the Y co-cordinates of the top and bottom nodes changes after I toggle between the "select and transform objects" and "Edit paths by node" modes.

The Inkscape version is 0.48, and the OS is Windows x64.

Sample file in which this problem is seen is attached.

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