I do not suspect that the command line tools have any effect on the behavior you observe. I was unable to reproduce the behavior on my MBP, but it might have different hardware. Wolfram support will probably ask you for this information as well, but it would aid my attempts to diagnose the problem if you could provide details about the machine on which you observe them. Specifically, it would be useful to know the Model Identifier, Display(s), and GPU(s). For example, here is the relevant details on my own machine from System Information:
Model Identifier: MacBookPro11,3
Processor Name: Intel Core i7
Processor Speed: 2.3 GHz
Intel Iris Pro:
Chipset Model: Intel Iris Pro
Type: GPU
Bus: Built-In
Displays:
Color LCD:
Display Type: Retina LCD
Resolution: 2880 x 1800 Retina
Retina: Yes
Pixel Depth: 32-Bit Color (ARGB8888)
Main Display: Yes
Mirror: Off
Online: Yes
Built-In: Yes
NVIDIA GeForce GT 750M:
Chipset Model: NVIDIA GeForce GT 750M
Type: GPU
Bus: PCIe