In PRM file you can tell linker how you want data to be aligned. For example
EEPROM = NO_INIT 0x0C00 TO 0x0FEF ALIGN 4;
makes all data aligned to 4 byte boundary. To align just long's:
EEPROM = NO_INIT 0x0C00 TO 0x0FEF ALIGN 1 [4:4];
Look for ALIGN in Built Tolls Utilities help