Yes I can reproduce this problem at will. It has something to do with when the aspect ratio of the game doesn't match the aspect ratio of the native resolution of the monitor, when playing in fullscreen mode. Alternatively, it may have something to do with the monitor switching its resolution when the game is not run at the native resolution. At any rate, the ships will have the proper aspect ratio when on the refit screen, but have an incorrect one in combat due to resizing. (Or the reverse.)
For example: my laptop's monitor has a resolution of 1366 x 768 (16:9 aspect ratio). If I play the game in fullscreen mode, at 1024 x 768 (4:3 aspect ratio) resolution, and I tell the display to maintain aspect ratio (i.e. black bars on left and right), then the refit screen (and the campaign map) will look normal, but the combat map will be thin; all ships will be tall vertically and squeezed horizontally. If I tell the display to stretch to fit, then the refit screen (and the campaign) will look "fat" (wider), while the combat map will be normal.
The fix is probably to keep the game at the same aspect ratio, i.e. assume that black bars on the left and right (in this case) is the "proper" way to display the game, and assume the player can adjust it that way on their monitor.