I've designed a custom PCB that I'm trying to program through ICSP using AVRISP mkII and I've run into some issues. I'm using Arduino IDE for programming, but I don't think this is relevant. The IDE says that the programming was successful, but the program does not run. I've tried with a few different programs using different pins, all with no luck. I had a different PCB before for the same application and it worked fine. In the second version of the PCB I used more pins on the CPU and thus needed to use the programming pins as GPIOs as well. I have some pull-down resistors on those lines, because they are driving MOSFETs. I suspect these resistors are the problem, but I haven't tried removing them since they are 0402 size and will be hard to solder back on in case I'm wrong. Am I right to think the pull-down resistors are the issue? Is there anything else I've missed?
I'll be grateful for any help I receive.