Atmega328 reset pin not working after re-burning Arduino boot loader?
There is a fuse on AVRs called RSTDISBL, which disables the functionality of the reset pin and allows you to use it as a normal I/O pin. If you program this fuse then resets will obviously not work and you will not be able to program the chip via ISP. This also means you can't unprogram the fuse via normal methods.

If this is the case then you can unprogram this fuse via High Voltage Programming. If you have an AVR Dragon board handy then you can do this easily by connecting the right pins on the HVSP header to your chip. Be careful if you're doing this in-circuit though, as the high voltage programming options uses 12 volts, which may fry the rest of your circuit. Best is to program it exclusively on the dragon via a ZIF socket or similar.

Here is a video from Atmel on how to unprogram the fuse via High Voltage Parallel Programming: http://www.youtube.com/watch?v=32CkOkpOcSc