AtMega32u4 flip usb verify problem

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Hey guys,


I'm using an AtMega32u4 chip with the LUFA DFU bootloader on it which I uploaded to the chip with Atmel studios and a AVRISPmk2 6 pin programmer. When I go to FLIP to burn the .hex file it won't verify a few times (usually between 3 and 5 times) then it finally will. The times it won't verify reading the .hex file of the atmega shows 32 lines of blank space that doesn't get programmed. Has anyone seen this before or know what would be is causing it? 


I'm using the LUFA bootloader because I need to be able to update the flash through USB without using ISP so if anyone could recommend other bootloaders that can be updated through USB without using HWBE since the board I have the HWB pin is floating.