Add the attached MEL script to your user script directory (i.e. My Documents/maya/5.0/scripts/). Restart Maya if you have it running. What will happen now is each time you minimize/maximize the viewpanels, the selection will refresh as per the script I posted earlier.

Tech notes for those who care:

panePop.mel is the MEL script that is run each time you hit the space bar to "pop" from multiple viewpanels to a single viewpanel and vice versa. The script is located in the scripts/startup directory of the Maya application directory (i.e. "Program File/AliasWavefront/Maya5.0/scripts/startup/"). All I did was copy panePop.mel to my user scripts directory and then add the 3 lines to save the selection, clear the selection, and reselect the previously select objects. Because user scripts override the application default ones, this customized version of panePop.mel will always run whenever you press the space bar.