chip45 bootloader in Atmega32U4

Good morning. I am using the chip45 bootloader for an Atmega chip. The chip being used is the Atmega32U4 chip (“chip45boot2_atmega32u4_uart1_v2.9Q”).

This is the datesheet of atmega32u4:http://www.componentschip.com/details/Atmel/ATMEGA32U4.html

I am having a strange error. I burn the bootloader with a success message from the AVR ISP. Then when I use the chip45 GUI it says no bootloader. Then I decide to see if there is anything written in my flash. I do a read of the flash. I see an anomaly. Almost everything is written except the last couple of lines. I think this is causing the error message I am pasting the actual boot and the read boot below.

Actual boot -

:107EE0000801811102C08BE201C08DE20E94463C74 :107EF000BCCDF999FECF92BD81BDF89A992780B586 :107F00000895DC01CB0103C02D910E948C3F4150AC :107F10005040D0F70895262FF999FECF1FBA92BD91 :107F200081BD20BD0FB6F894FA9AF99A0FBE01965A :027F30000895B2 :040000030000780081 :00000001FF

Read boot -

:107EE0000801811102C08BE201C08DE20E94463C74 :107EF000BCCDF999FECF92BD81BDF89A992780B586 :107F00000895DC01CB0103C02D910E948C3F4150AC :107F10005040D0F70895262FF999FECF1FBA92BD91 :107F200081BD20BD0FB6F894FA9AF99A0FBE01965A :107F30000895FFFFFFFFFFFFFFFFFFFFFFFFFFFFB2 :107F4000FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF41 :107F5000FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF31 :107F6000FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF21 :107F7000FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF11 :107F8000FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF01 :107F9000FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF1 :107FA000FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFE1 :107FB000FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFD1 :107FC000FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFC1 :107FD000FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFB1 :107FE000FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFA1 :107FF000FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF91 :00000001FF

Sir, as you can see from above, after the line (“:107F200081BD20BD0FB6F894FA9AF99A0FBE01965A”) there is some confusion. Have any of you encountered such an issue before. I then tried checking if anything is wrong with the clock and such. I am able to program the chip and also toggle a pin using the AVR studio.

I know its a very narrow doubt which I should ask chip45 directly, but in case anyone can help me it would be great.

Thank you.