Not sure if this is your specific problem, but first you zero out memory:

memset(c->ram, 0x00, 65536);
memset(c->basic_rom, 0x00, 8192);
memset(c->char_rom, 0x00, 4096);
memset(c->kernal_rom, 0x00, 8192);

Then you try to initialize the program counter by reading from memory:

c->pc = (rb(c, 0xFFFD) << 8) + rb(c, 0xFFFC);

Seems questionable - it'll always be initialized to 0!

I assume somewhere else you're loading your program into memory, otherwise of course it'd always execute BRKs - that's all there is.

It's hard to say if this is an initialization error or an error elsewhere. You say:

even though the PC has a different value

Have you tried debugging the process by which you fetch data from memory at the PC?