I think you have to running out of memory and clobbering something. Do you still allocated large arrays?
When you compile locally with make clean all, what are the last lines out? Something like this:
arm-none-eabi-size --format=berkeley core-firmware.elf
text data bss dec hex filename
83164 2964 11500 97628 17d5c core-firmware.elf
The RAM used is data+bss; the FLASH used used text+data.