Brand new MacBook Pro- tons of permissions errors

So I just got a brand new MacBook Pro but am having some issues with it. I installed StarCraft 2 but will encounter a black screen that is unresponsive to anything (option-command-esc, for example), when I exit the program and once when I went to view a replay. I have to hold the power button down.
Blizzard told me that I should try to repar my permissions. Every time I do this, however, I get the same errors and they are never fixed. I don't know if this is causing my problem but this computer is brand new and I shouldn't have all these permission errors.
Here are the messages that I get:
Verify permissions for “Macintosh HD”
Permissions differ on "System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Classes/dt.jar", should be lrwxr-xr-x , they are lrw-r--r-- .
Permissions differ on "System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Classes/jce.jar", should be lrwxr-xr-x , they are lrw-r--r-- .
Permissions differ on "System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Classes/jconsole.ja r", should be lrwxr-xr-x , they are lrw-r--r-- .
Permissions differ on "System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Classes/management- agent.jar", should be lrwxr-xr-x , they are lrw-r--r-- .
User differs on "System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home/lib", should be 0, user is 95.
Permissions differ on "System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home/lib/dt.jar", should be -rw-r--r-- , they are -rwxr-xr-x .
Permissions differ on "System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home/lib/jce.jar", should be -rw-r--r-- , they are -rwxr-xr-x .
Permissions differ on "System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home/lib/management -agent.jar", should be -rw-r--r-- , they are -rwxr-xr-x .
Permissions differ on "System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home/lib/security/b lacklist", should be lrwxr-xr-x , they are lrw-r--r-- .
User differs on "System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Libraries", should be 0, user is 95.
Permissions differ on "System/Library/Java/Support/Deploy.bundle/Contents/Resources/JavaPluginCocoa.b undle/Contents/Resources/Java/deploy.jar", should be lrwxr-xr-x , they are lrw-r--r-- .
Permissions differ on "System/Library/Java/Support/VisualVM.bundle/Contents/Home/profiler3/lib/deploy ed/jdk15/hpux-pa_risc2.0/libprofilerinterface.sl", should be -rw-r--r-- , they are -rwxr-xr-x .
Permissions differ on "System/Library/Java/Support/VisualVM.bundle/Contents/Home/profiler3/lib/deploy ed/jdk15/hpux-pa_risc2.0w/libprofilerinterface.sl", should be -rw-r--r-- , they are -rwxr-xr-x .
Permissions differ on "System/Library/Java/Support/VisualVM.bundle/Contents/Home/profiler3/lib/deploy ed/jdk16/hpux-pa_risc2.0/libprofilerinterface.sl", should be -rw-r--r-- , they are -rwxr-xr-x .
Permissions differ on "System/Library/Java/Support/VisualVM.bundle/Contents/Home/profiler3/lib/deploy ed/jdk16/hpux-pa_risc2.0w/libprofilerinterface.sl", should be -rw-r--r-- , they are -rwxr-xr-x .
Permissions differ on "System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Classes/dt.jar", should be -rw-r--r-- , they are lrw-r--r-- .
Permissions differ on "System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Classes/jce.jar", should be -rw-r--r-- , they are lrw-r--r-- .
Permissions differ on "System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Classes/jconsole.jar ", should be -rw-r--r-- , they are lrw-r--r-- .
Permissions differ on "System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Classes/management-a gent.jar", should be -rw-r--r-- , they are lrw-r--r-- .
Permissions differ on "System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Home/lib/dt.jar", should be lrwxr-xr-x , they are -rwxr-xr-x .
Permissions differ on "System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Home/lib/jce.jar", should be lrwxr-xr-x , they are -rwxr-xr-x .
Permissions differ on "System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Home/lib/management- agent.jar", should be lrwxr-xr-x , they are -rwxr-xr-x .
Permissions differ on "System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Home/lib/security/bl acklist", should be -rw-r--r-- , they are lrw-r--r-- .
Permissions differ on "System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Resources/JavaPlugin Cocoa.bundle", should be drwxr-xr-x , they are lrwxr-xr-x .
Permissions differ on "System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Resources/JavaPlugin Cocoa.bundle/Contents/Resources/Java/deploy.jar", should be -rw-r--r-- , they are lrw-r--r-- .
Permissions differ on "System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Resources/JavaPlugin Cocoa.bundle/Contents/Resources/Java/libdeploy.jnilib", should be -rwxr-xr-x , they are lrwxr-xr-x .
Warning: SUID file "System/Library/CoreServices/RemoteManagement/ARDAgent.app/Contents/MacOS/ARDAg ent" has been modified and will not be repaired.
Permissions verification complete

I did do a search for a similar topic and I did read that some permissions are of no concern. However, like I said the guys at Blizzard said that it could be the source of the issue. Also, like I said, even if I do "repair permissions" and it says that it completes successfully, it has not really done anything. Even if I run verify permissions immediately after, I see the same problems.

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