hi,
I know the one reason of your problem because had it myself.
As you know, RB2 contains 16K Bytes of program memory organized in 128 pages of 128 Bytes. It means that flash must be programmed page-by-page. Remember it and read below.

When Keil (or other compiler) generates hex file it does not pay attention about 128-bytes align. It just generates lines and writes them to a file. Now your custom-made software tries to program flash. It reads lines from hex-file and sends them via UART to a part. But these lines are not aligned! Bootloader software does not aling received data itself, it just put data into column latches and runs hardware programming. As result, some data which goes over the align borders, are placed at wrong addresses.

FLIP aligns all data from hex-file internaly. I know it due I asked for such issue to Atmel.

All you need is read data from hex-file and then keep them aligned at 128-byte pages while send them to a chip.

Good luck,
Oleg