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In fullscreen in RC5, the mouse cursor seems to be displayed somewhat higher than it actually functionally is. For example, if I hover over the "Credits" menu, the "Exit" menu is highlighted.
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After running in windowed mode with a custom resolution, I started FO RC5 from the start menu link as fullscreen. The in-game resolution setting still showed my custom window size, however, not the actual resolution I was using (1024x768).
After re-setting the resolution in-game to something else, I quit and restarted. Then the mouse cursor position was displayed correctly, while in fullscreen mode.
I suspect the misplaced mouse cursor is related.
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I can't reproduce the mouse being in the wrong place in fullscreen mode. This has been reported many times, but I've never seen it.
When the in-game resolution setting reported the wrong size, were you looking at the spin boxes, or the drop-list? The spin boxes are supposed to retain their old values, but the drop-list should have said 1024x768 @ 32 bits (fullscreen), or similar.
After starting in windowed, setting a custom resolution, quitting, starting in fullscreen, the resolution options droplist says "Custom". The spinners to indicate resolution say the values form the windowed case. The "Fullscreen" checkbox is checked (which is correct).
The cursor position part should only be fixed in the ogre-integration branch, which draws its own cursor instead of using the hardware cursor. This guarantees that the cursor is drawn exactly where GG thinks it is, so the input and display always match.
Fixed in GG Subversion. (The fix wasn't in the FreeOrion code
itself, but in GG, the GUI library FreeOrion uses.)