Cannot see certain parts behind transparent objects

[Aaronm87]

So I have been having a weird issue lately where some objects cannot be seen when they rare behind another object that is transparent. Unfortunately, I cannot upload any images of the real model, but hopefully the attached image helps explain. Basically, I can see objects A and B behind other transparent components, but then randomly in different assemblies component B cannot be seen. (A and B being multiple parts and assemblies, not just a single assembly). No pun intended, but has anyone seen this issue before? 

Update: There are existing components in the assembly that when moved can be seen. However, when I copy the same object, it cannot be seen.

[StephenW]

It's gonna be pretty difficult to help without something. Possibly you could make some test data to illustrate the problem without real components.

My first guess would be color/transparency settings on the components is too similar but that's like a shot in the dark.

[dschenken]

I would first look to see if the missing part interferes with another part such that the shader cannot tell which is in front of the other.

[Aaronm87]

Interference doesn't seem to make a difference. Even if I move the part so that it protrudes out of the transparent component, it displays the external portion correctly and the internal portion is still invisible.

I did find a work around. If I set the object as transparent AND select an individual surface as transparent the part displays as it should. Only issue is the transparency isn't at the same level, even though the same material was used on all transparent parts.