it's not unusual - there are some things you can try:
1) did you check the "frame adaptation" box in StarAlignment? without that SA will not attempt to match the brightness between panels.
2) even with frame adaptation, sometimes things still look wrong due to gradients; you might try running DBE on both images before combining to make sure they are gradient free
3) there's a script out there called "dnaLinearFit" (by david ault) which will compute the intersection between two panes and run linear fit on them. this together with DBE should guarantee that your frames have similar background brightness when going into StarAlignment.
rob