This could be your answer. The PNG format tiles are not compressed. We recommend using "mixed JPGPNG" format, which uses JPG for all tiles *except* those that have pixels labeled as transparent. Using any compression method (JPG, ECW, MrSID, others), if a pixel is 0, the compression may change that to a 1 or a 2 (still very dark black). If 0 is supposed to be treated as transparent, the compressed nonzero values will no longer treated as NoData in ArcGIS (a.k.a. transparent). For those (typically few) tiles with NoData values, they'll be written as PNG, but the majority will be JPG.
Try reprocessing a SUBSET (not the entire dataset!) and use format = JPGPNG.
If you have a lot of NoData pixels within the interior of your dataset, this may require further discussion.