I compared the files again and the only differences are in the last 4 lines.

Here are the last 4 lines of the written file:
:0C03D0000D300C1EE92999006029630023
:04400E00622FFF3FDF
:00000001FF
;PIC16F88

And here are the last 4 lines of what comes back from the read:
:1003D0000D300C1EE929990060296300FF3FFF3FA3
:08400000FF3FFF3FFF3FFF3FC0
:04400E00622FFF3FDF
:00000001FF