Accessing Serial while using a battery as a power source

I'm using codebender.cc as my IDE, primarily because the crappy Java IDE is unreadable on a High DPI screen.

I'm able to use Serial functions, but when I have an external battery connection via VIN I get strange behavior; Sometimes I can connect to the Serial and watch my println statements. Other times I can't. Sometimes I can start monitoring and then connect the battery and it will work, but it's been difficult to find a pattern.

I've also noticed that I can sometimes get it working with a 9V battery, but a 12V battery rarely works, I think I've had a 3% success rate with 12V.

Amy suggestions?

Amy suggestions?

Post your code and a schematic for a start.