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Whenever you generate a jedec file from CyClocks for CY2292F, it adds in date code information on the last line of the file. This causes the differences in checksums for the same configuration. So generating a JEDEC file from the software will give you a different JEDEC checksum due to the last line in the JEDEC file that contains time and date information. All of the other lines above in the JEDEC should match though. The bits contained in rows 100-140 do not configure the device. It is date code information which is not necessary and can be ignored. If you compare all of the other lines in the JEDEC file they will be the same for the older devices, the factory programmed devices, and the field programmed devices.