I have 5 excel files open. If I click on Add to group > All ungrouped windows from Excel.exe OR Add to group > All ungrouped windows from XLMain, Groupy only groups 3 Excel windows even though 5 Excel windows are open. I have to manually add the others to the group.
I tested with 7 Word document windows and it does the same thing i.e., group only 3 windows. It appears this option groups only 3 windows, that appears to be a limitation in Groupy right now or maybe a bug. Groupy should group (as the name of the action suggests) all ungrouped windows regardless of how many there are.
I am guessing this happens with other applications as well though I did not test.