Hey CA, i have learned a stupid little emotional problem that arduino seems to have. While i do not understand the why, It is well documented if you just search around for it. If you open your arduino file by double clicking on the file itself, then there is a good chance it will not write to the board. However, if you just open the arduino ide first. and then open the file from the arduino environment suddenly things work and write. Wierd problem but very simple fix. I'm not sure if that is what you are describing or not.