Got you email but was about to respond here
Yes we can see the issue. Although you board package incles the correct gcc toolchain the package is defined to ignore it and use inheritance to find the toolchain in another package (stm32duino).
Visual Micro is finding the correct arm-gcc version in both the arduino samd tools and also the stm32duino tools. Visual Micro then uses the wrong version from arduino instead of stm32. Although the arm-gcc version numbers are the same the arduino version doesn't work with your board.
The arduino ide ignores your toolchain and instead uses the smt32duino toolchain :-
C:\Users\[your 2014q1
but you will see in the output that visual micro is using :-
C:\Users\[your 4q1
Potential Short Term Workarounds
We will release a fix for this during the next week but you can probably solve it yourself a few ways. These workarounds might not be suitable but give ideas.
1)
Your custom package does actually install the correct tool chain version. It is possible that adding the following local project board.txt property (or the platform.txt in the package) will force the correct toolchain to be used.
runtime.tools.arm-none-eabi-gcc.path=C:\Users\[your cc\4.8.3-2014q1
2)
If you don't need Arduino samd boards before the fix is released then you can uninstall the arduino samd package and then we should resolve either the stm32duino or your custom toolchain. both are the same.
To uninstall the arduino 3 bit boards you can delete this folder then click Rescan or restart the ide:-
C:\Users\[your name]\AppData\Local\arduino15\packages\arduino
Based on the fact that you do not currently have the .hson index url for the arduino package in your list I suspect option (2) will be the easist because you don't use the arduino boards (arduino zero/due etc)
Does this make sense.