which tools are you trying to use? Are they declaring their requirement like this (in the tool wrapper .xml files):
<requirement type="package" version="3.4">python3</requirement>
In addition, I just checked the toolshed recipe for the package_python_3_4 installation and I think it does not automatically make the installed zlib available at runtime. So maybe a tool using zlib-dependent functionality of python3 should also include the requirement declaration:
<requirement type="package" version="1.2.8">zlib</requirement>
You could try adding this line to the requirements section of the tool wrappers and just see what happens.