When I updated to Jessie, I no longer was able to program the ATmega328P on the Gertboard. I had been using my own python program to upload the .obj code from the avra assembler to the ATmega328P using the connections shown in the Gertboard instructions (page 43). It seems that in Wheezy, my program was able to override the spi driver control of GPIO8 using a GPIO output command so that GPIO8 was held low for the entire time the code was being uploaded. With the Jessie driver, it appears that I need to use GPIO7 instead of GPIO8 for uploading programs because the Jessie driver raises GPIO8 occasionally causing the ATmega328P to start executing the partial code. The RESET line which enables programming of the ATmega328P must remain down for the entire upload.
I don't know whether this problem affects avradude since I have never used it.
My explanation might not be right, but what is clear is that the two drivers do things slightly differently and the differences can affect programs after an upgrade to Jessie.