The following errors appear when scanning stacked switches with Switch Port Mapper:
Disable GetBulk to let Switch Port Mapper request one value at a time.
1. Go to Switch Port Mapper and click Settings.
2. Click the Port Map Settings tab.
3. Uncheck the Use GetBulk option in the Switch Settings and Layer 3 Device Settings sections, and then click OK.
This should slow down the queries and allow the device to keep up.
When using GetBulks, Switch Port Mapper requests 20 values at a time. With stacked switches, these requests can pile up and eventually the time for the switch to respond is greater than the time Switch Port Mapper is willing to wait.