I wish I knew. It seems like it's some setting since it keeps happening regardless of format.
Perhaps the trees are being imported as terrain to which surface opacity is much less than 100%, or perhaps they're being imported with an inverted transparency, yes?
There are a few places that can happen:


If the surface opacity is less than 100% some part (all, really) of the surface will have that much transparency.
Also, there are styles that have elements of transparency:

Also and importantly, the source file for the trees must be free of things that would cause transparency issues. In fact, the source file is the most important element of any data import for Infraworks.
Other odd-ball ways to get this include inserting the trees below ground (it is possible). This can be checked by clicking on the tree, right clicking to get properties, and check the insertion coordinates. Another might be having existing grade far below the proposed grade, but the models surface data does not yet include the new grade, so, pick and click finds the old ground and not the new, so the trees are below the new grade and look, well, weird.
That can be fixed with this:

Lock your mouse above ground. The trees can be fixed through their properties.
Tough nut to crack. I had a lot of trouble figuring this program out when I was first introduced to it.
I'm convinced it's a setting, though. Has to be. The program doesn't malfunction this way. It messes up lots of ways, but this isn't one of them.
Wish I had better to offer.