Thanks for your reply ApolloBoy, I definitely have the board connected correctly and double checked my connections several times before commiting to soldering, and its connected to a 47 inch Vizio 120hz set (turned off smooth motion, set to game mode)
I should add, the Jr has given me a problem in the past with it going all wavy/static, more so when touched while on. After the AV mod, its so much cleaner looking but I can now see this problem, I'm starting to think its had this issue for a while, just unoticable using the old RF connction perhaps?
I did just aquire a really nice heavy sixer that even with the RF connection has a nice picture. I'm leaning towards removing the mod out of the atari jr and install it in that.