This happens when your innermost column dimension contains protected groups and the numbers displayed in group member cells do not total up to the total displayed in the group cells.
It can also happen if your total does not include all the items in the dimension are not included in the defined dimension total. For example, in the People.ivt sample table that comes with the Beyond 20/20 Browser, the cities in the REGION dimension are not included in the country totals and therefore are not included in the North American total. For this reason, percentages for North America on the REGION dimension are not 100.