wishywashy:
Fantastic. Atleast I know what the issue is now. Also I know this is probably stupid but is the Flash memory like the EEPROM and have a certain amount of reads and writes?.
Writes? Yes. But this shouldn't be an issue because the only time you are writing to the Flash memory is when you program the chip. A bug in a sketch that writes to the EEPROM might accidentally use up it's lifetime fairly quickly, so that is why the lifetime of the EEPROM (which, incidentally is actually longer than the lifetime of the Flash memory) is stressed so much. A tight loop that writes to memory location 0 of the EEPROM every 1ms will run through the life of that memory cell in less than 2 minutes...
Reads? No, for both EEPROM and Flash memory.