Intel MKL FATAL ERROR when running Anaconda projects in 2017.3 Python/PyCharm

I recently upgraded to 2017.3 and nothing else changed (that I can see) and now when I run pytest or in general a script in the IDE I get the following error:

C:\Anaconda3\envs\backtrader\python.exe C:/dev/trading/engine.py
Intel MKL FATAL ERROR: Cannot load mkl_intel_thread.dll.

Process finished with exit code 2

It Seems quite odd when I run that on my command line it works. Same for py.test fixtures, using the supplied command line from the window I can run a py.test suite on the command line but in the IDE it just says no tests found.

Is the Scientific Mode playing up with normal code, as this is the only thing I can see being different? 

Any help would be appreciated as this is incredibly hard to work with, I'll probably have to to back to 2017.2 if it still persists.