-Confirmed-
Many of these transparency issues cannot be solved due to the rendering engine used, (OpenCL) You will see many of these issues in minecraft too, So i've heard.
However, none the less, Lets see what schema can do.
I was able to reproduce the transporter transparency issue and the cargo issue and I've seen the transparency issues with salvage beams.
Steps to reproduce transporter:
Use a teleporter with shields nearby, The warp affect that comes up from under you makes force fields disappear.
Steps to reproduce cargo blocks:
Put some cargo blocks behind glass make sure they are filled.
As for the salvage I've seen that happen all to many times on my HD 6750, But i was unable to reproduce that on my GTX 760.
Cargo issue
{F5756}
Transporter issue
{F5758}
{F5760}