I've seen an issue like this, but only with a coverglass. If the coverglass is not exactly parallel with the sensor, you can get some issues wiht symmetry.
But the light goes out in a symmetric cone, and unless you have a tilted coverglass you should get the same answers.
(I'm assuming when you rotated the sensor you switched from an 8x16 to a 16x8.)
Try the same experiment without the coverglass. Or use the crosstalk free glass that was included with the Eval kit. Does that work better?
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