Well as you didnt flash emmc, then old settings and configs dont get erased, and that behaviour is expected, so its your own fault . If you only flash main.bin then you need to add --erase-user-data=secure. So either:

"sudo flasher -f -F firmware.bin --erase-user-data=secure ; sudo flasher -a firmware.bin -k zImage_2.6.32.54-openmode_l2fix --flash-only=kernel -f -R"

or if you also have emmc.bin then:

"sudo flasher -f -F firmware.bin -F emmc.bin; sudo flasher -a firmware.bin -k zImage_2.6.32.54-openmode_l2fix --flash-only=kernel -f -R"