Programo la flash:

C:\WinAVR\bin>"avrdude" -p m88 -c sp12 -P lpt1 -U flash:w:"C:\at88loader.BIN":a -F

avrdude: AVR device initialized and ready to accept instructions

Reading | ################################################## | 100% 0.00s

avrdude: Device signature = 0x1e930a
avrdude: NOTE: FLASH memory has been specified, an erase cycle will be performed
To disable this feature, specify the -D option.
avrdude: erasing chip
avrdude: reading input file "C:\at88loader.BIN"
avrdude: input file C:\at88loader.BIN auto detected as raw binary
avrdude: writing flash (8192 bytes):

Writing | ################################################## | 100% 3.58s

avrdude: 8192 bytes of flash written
avrdude: verifying flash memory against C:\at88loader.BIN:
avrdude: load data flash data from input file C:\at88loader.BIN:
avrdude: input file C:\at88loader.BIN auto detected as raw binary
avrdude: input file C:\at88loader.BIN contains 8192 bytes
avrdude: reading on-chip flash data:

Reading | ################################################## | 100% 2.95s

avrdude: verifying ...
avrdude: verification error, first mismatch at byte 0x0000
0xff != 0x00
avrdude: verification error; content mismatch

avrdude: safemode: lfuse changed! Was e0, and is now ff
Would you like this fuse to be changed back? [y/n] n
avrdude: safemode: hfuse changed! Was df, and is now ff
Would you like this fuse to be changed back? [y/n] n
avrdude: safemode: efuse changed! Was 0, and is now 7
Would you like this fuse to be changed back? [y/n] n
avrdude: safemode: Fuses OK

avrdude done. Thank you.

Los fuses si están bien, si te fijas no hay ningún error, pero en la flash si lo hay.
Repite hasta que no salga error, prueba otra vez con el avrdude-gui, indícale que el bin está en C

saludos.