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The odom frame is attached to the world. So as the robot drives around, it is going to be in a different position/orientation relative to the odom frame. On startup it just happens to be that the robot is turned 90 degrees relative to the odom frame, but this angle will change as the robot moves around.
The navigation goals you send to the robot are specified in the odom frame. So you tell the robot where to go in absolute world coordinates. It sounds like you want to command the robot in relative coordinates (move 1 meter forward from where ever the robot is right now). To do that, you have to convert the relative goals in absolute coordinates. Tf can help you do this.
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