Hi Pencilart, I have not noticed any wrong interpretation of transparency values in sh3d. Not obj/mtl interpretation, not texture interpretation.
1) did you check the .mtl file that accompanies the .obj file? Correct transparency should be set as d value under the transparent material. Eg.
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d 0.0 (=fully transparent - invisible)
or
d 0.5 (=semi transparent 50%)
2) did you check the texture file (if you use one - png/gif) to see whether it still has transparency after export?
ok