@whale-av you are absolutely right. I have two machines with same os, pd, libs versions but different hardware. On the problematic machine I installed pd in a ubuntu 17.10 virtual machine and pd patches look correct. Should be a bug in the video driver version included with Ubuntu 16.04 LTS.
Number and symbol boxes look funny. Angled connections are not rendered. Creating and editing patches are impossible due to lack of visual feedback.
pd vanilla: 0.46.7
tcl, tk: 8.6
I suspected tcl/tk 8.6 being the culprit. I couldn't replace them with 8.5 as one of the dependencies of puredata-gui installs 8.6. Besides, I have another system with the same versions as this one but works without this issue.
Has anyone experienced the same issue? Any idea how to fix it?