There are two issues that may cause this to happen.
1. The reading from the Differential Voltage Probe, order code DVP-BTA, $39 is not centered around zero (0). You can determine this by studying the reading from the Voltage Probe when both solar panels are in the same amount of light. To correct this you can change the "Comparison" value in your program to match the value you note in these circumstances.
2. Your solar panels may need a different size resistor in order to get sufficient voltage for comparison. In order to get a resistor of the correct size try this:
a. Obtain a variety of resistors for comparison. We recommend trying resistors in the neighborhood of 50, 100, 200, and 300 ohm.
b. Using a single solar panel, connect the red and black leads to either side of a resistor.
c. Create a simple program to read the Differential Voltage Probe and connect the differential voltage to the Brick with the Vernier adapter.
d. Attach the red and black leads of the Differential Voltage Probe to the red and black leads of the solar pane.
e. Start the program and note the voltage.
f. Shine a flashlight on the solar panel. Note the voltage again.
g. Repeat this process for each resistor. Choose the resistor that gives you the biggest voltage change and wire your solar tracker with a pair of those resistors.
LEGO® MINDSTORMS® Education EV3 Core Set with Charger, order code LEGO-EV3-CORE, $412
NXT Sensor Adapter, order code BTA-NXT, $39
Vernier Engineering Projects with LEGO® MINDSTORMS® Education EV3 (Electronic Version), order code EP-EV3-E, $40
TIL 3339: LEGO® Mindstorms® EV3 Troubleshooting and FAQs