a timer, or any other device put inline between the power source and ballast will act as a resistor and lower the amount of power going to your bulb, so yes it could make the bulb burn irregular... the larger the gauge of wire, and better quality the connections are of any device put inline between your equipment and power source, the less power will be loss due to resistance...
ever pluged a power tool into an extention cord that was really long, sometimes the tool wont work properly, and may even throw the breaker
power works best with the least amount of resistance, thats whay some ballasts say the max length the power cord to the socket can be, because even the cord has resistance...