When you have 2 glyphs (for example A and W) selected in the Kerning wizard, it needs to calculate 2*2 = 4 possible kerning pairs:
AA
AW
WA
WW
When the user selects 256 glyphs, it has to go through 256 * 256 = 65536 possible kerning pairs. That would take a long time and then you most likely will run into the maximum kerning pairs limit of 10920.
Within the Automatic Kerning wizard do try to use a predefined kerning pair file (kern_standard.txt or kern_extended.txt) and see if that works for you.