EDK base system builder design for Spartan-3E Starter Kit uses the value 70300 for C_DDR_TREFC (Refresh command interval) parameter. According to the IP data sheet, this value is defined in terms of ps and according to the micron data sheet for the DDR memory device on board, this value should be 70.3 us.
This is an inconsistency in the "Base System Builder" design with the DDR data sheet. Please change it to 70300000 for the parameter value. But functionally speaking, the OPB DDR controller works with this smaller refresh interval.