I have this little problem too. What I do is select the Battlestar and dock the Viper. Once docked, exit and locate the viper. Once youve found it, hover over it with the mouse and record its current position eg (706.9, 61.9, 842.7).
Once youve got that information, select the battlestar again and undock the viper...... you'll notice its pitch, bank and heading will still be properly aligned.
Select the Viper and press shift-o and input your positional info and hit ok. Tadaa, the Viper should be perfectly in position.
Note this will only work if the docking and undock info is changed through the Battlestars Intial status. If done through the Viper, the Battlestar will move instead.
Hope this helps.