Usually different polygons using different materials stay that way.. could it be because of the summarized level of polygons you might have to increase the Light Path -> Max Bounces values for transparency or total ( i assume cycles ) ??
okay where would I apply scale and rotate. in the transform option I hit apply all transforms. Also I maxed everything I could in light path because I wasn't sure what option you wanted adjusted only result I got from doing this was making him bald
Menu -> Object -> Apply -> All Transformations or shortcut Ctrl-A. Could it be that the top strands to have some modifier added ?? Because they do not get merge.. you may have to copy this to the main object first by selecting the main object first and then the hair Object -> Link/Transfer Data -> Copy Modifiers (from all to the last one) and for joining reverse the selection ( join to the last one).
I was able to figure it out, The issues that has caused all the problems was from combining objects with differnt UVs. Select the object > In The Properties menu on the right (Up-side-down green triangle) > UV Maps drop down > Change UV name to the one used by the other objects (MUST BE EXACT - Can delete hidden UVs as well) > Then Merge objects and everything will work perfect
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Ohh... and i hope both objects have their scale and rotation applied so there is no "different/wrong" reflection via a shader.
Could it be that the top strands to have some modifier added ?? Because they do not get merge.. you may have to copy this to the main object first by selecting the main object first and then the hair Object -> Link/Transfer Data -> Copy Modifiers (from all to the last one) and for joining reverse the selection ( join to the last one).