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Added in build 2020, you can now use the "gutterForeground" key in .tmTheme files
Should be fixed in build 2020
A shadow is now added when required to separate the minimap from the buffer
Can you confirm which version you're using? I believe this problem was fixed in 20110203.
Only for Linux and Windows. It'll be in the OSX key bindings too in the next version.
Python's subprocess module, which is used to implement the exec command, and hence the build systems, supports a parameter shell=True (False by default), that may well do what you want.

If you're feeling keen, can you try editing Packages/Default/, line 25, add the shell=True parameter, and see if that works for you?

If so, I can easily add 'shell' as a parameter in .sublime-bulid files
I believe that this is correct for the way OS X works: .profile is parsed by the shell, and neither Sublime Text X nor the spawned process is a child of any shell process, so I would not expect .profile to be parsed at any point. Let me know if my understanding is incorrect.
I don't seem to be able to replicate this: when I follow the instructions, I get taken back to the original file, and it has input focus.