That problem hasnt got anything to do with your computer. Its warcrafts 'problem'.
Computer players work same way as human players in a way. When you tell a computer player to move 100 units at same time, the comp player does the same thing you would do; he selects 12 units (max unit number which you can select) and orders them to move, then he selects another 12 units and orders them to move etc. etc.
There is no solution to this problem, except that you can (if your map allows) make more computer players and divide the units for the other computer players making each comp player to move less units, like 25 units for each comp (4 comps).