It does work with another app that just blinks an LED.
I'm using a pic32mx170f256b.
In the linker scrips, I changed the defined memory sections:
for the App (this was after i tried to move the startup code to program memory):
kseg0_program_mem (rx) : ORIGIN = 0x9D00F000, LENGTH = 0x30000
exception_mem : ORIGIN = 0x9D03F000, LENGTH = 0x1000
debug_exec_mem : ORIGIN = 0x9D000490, LENGTH = 0x760
kseg0_boot_mem : ORIGIN = 0x9D000490, LENGTH = 0x0
kseg1_boot_mem : ORIGIN = 0xBD000000, LENGTH = 0x490
and for the "bootloader":
kseg0_program_mem (rx) : ORIGIN = 0x9FC004B0, LENGTH = 0x650
exception_mem : ORIGIN = 0x9D03F000, LENGTH = 0x1000
/* I wasn't sure where to put exception_mem. I tried both boot mem after the bootloader and program mem*/
debug_exec_mem : ORIGIN = 0x9FC00AF0, LENGTH = 0x100
kseg0_boot_mem : ORIGIN = 0x9FC00AF0, LENGTH = 0x0
kseg1_boot_mem : ORIGIN = 0xBFC00000, LENGTH = 0x490
other than that i didn't change anything about the files, and my bootloader doesn't contain any config words (but i did leave them defined in the linker)