Also make sure you are in the BIN file mode type. Insert the source chip into the programmer and flip the lever on the ZIF socket - If there are any empty holes they should be near the lever end of the socket. If you are trying to load a Hex file on an Atmel remember that those parts have an automatic erase cycle which will cause problems with Hex segments as they load. Save your object code as a binary file and try again. You might try filling the buffer with 00s.
Hex files can also give bad check sums if they over write the same address space.
This is used increase program pulse time. Sometimes needed for very fast computers. The windows version has pretty much gotten around the need for this. Again, intended for use with some very fast computers. So don't mess with it.