Go to the SH3 folder in My Documents and find data/cfg/GameplaySettings.cfg, and open with Notepad. At the bottom you'll see:
[MiscSettings]
AlwaysAutotargeting=0,0,0,0,0;for warships, merchants, uboats, air and, respectively, land targets
Ensure that all the numbers are set to '0' for the window to appear when close to an enemy unit. The other settings I believe are:
1 = Maintain current orders.
2 = Engage target.
3 = Periscope Depth.
Good luck!
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