diff --git a/__tests__/SetupStore-test.js b/__tests__/SetupStore-test.js
index de3c2d4dd1..8b5052e699 100644
--- a/__tests__/SetupStore-test.js
+++ b/__tests__/SetupStore-test.js
@@ -77,15 +77,18 @@ describe('SetupStore', function () {
       machine.isoversion.mockReturnValue('1.0');
       machine.stop.mockReturnValue(Promise.resolve());
       machine.start.mockReturnValue(Promise.resolve());
+      machine.regenerateCerts.mockReturnValue(Promise.resolve());
       machine.upgrade.mockReturnValue(Promise.resolve());
       setupUtil.compareVersions.mockReturnValue(-1);
       machine.create.mockClear();
       machine.upgrade.mockClear();
       machine.stop.mockClear();
       machine.start.mockClear();
+      machine.regenerateCerts.mockClear();
       return setupStore.steps().init.run(() => {}).then(() => {
         expect(machine.create).not.toBeCalled();
         expect(machine.stop).toBeCalled();
+        expect(machine.regenerateCerts).toBeCalled();
         expect(machine.start).toBeCalled();
         expect(machine.upgrade).toBeCalled();
       });
diff --git a/package.json b/package.json
index 26bfa16ef5..7ae0f34fd4 100644
--- a/package.json
+++ b/package.json
@@ -40,7 +40,7 @@
     ]
   },
   "docker-version": "1.5.0",
-  "docker-machine-version": "0.1.0",
+  "docker-machine-version": "0.1.0-kitematic-0.5.8",
   "atom-shell-version": "0.21.2",
   "virtualbox-version": "4.3.24",
   "virtualbox-filename": "VirtualBox-4.3.24.pkg",
diff --git a/src/DockerMachine.js b/src/DockerMachine.js
index 4e587d2921..326d963574 100644
--- a/src/DockerMachine.js
+++ b/src/DockerMachine.js
@@ -83,6 +83,9 @@ var DockerMachine = {
       return Promise.resolve(stdout.trim().replace('\n', ''));
     });
   },
+  regenerateCerts: function () {
+    return util.exec([DockerMachine.command(), 'tls-regenerate-certs', '-f', NAME]);
+  },
   state: function () {
     return DockerMachine.info().then(info => {
       return info ? info.state : null;
diff --git a/src/SetupStore.js b/src/SetupStore.js
index 90d23fba71..ca575abcf9 100644
--- a/src/SetupStore.js
+++ b/src/SetupStore.js
@@ -61,7 +61,7 @@ var _steps = [{
   message: 'To run Docker containers on your computer, Kitematic is starting a Linux virtual machine. This may take a minute...',
   totalPercent: 60,
   percent: 0,
-  seconds: 53,
+  seconds: 58,
   run: Promise.coroutine(function* (progressCallback) {
     setupUtil.simulateProgress(this.seconds, progressCallback);
     yield virtualBox.vmdestroy('kitematic-vm');
@@ -86,6 +86,7 @@ var _steps = [{
       yield machine.upgrade();
     }
     yield machine.start();
+    yield machine.regenerateCerts();
   })
 }];
 
diff --git a/src/SetupUtil.js b/src/SetupUtil.js
index e626958b0a..95fe6c0b5f 100644
--- a/src/SetupUtil.js
+++ b/src/SetupUtil.js
@@ -13,15 +13,15 @@ var SetupUtil = {
       return true;
     }
 
-    if (!fs.existsSync('/usr/local/bin/docker') || !fs.existsSync('/usr/local/bin/docker-machine')) {
-      return fs.statSync('/usr/local/bin').gid !== 80 || fs.statSync('/usr/local/bin').uid !== process.getuid();
-    }
-
-    if (fs.statSync('/usr/local/bin/docker').gid !== 80 || fs.statSync('/usr/local/bin/docker').uid !== process.getuid()) {
+    if (fs.statSync('/usr/local/bin').gid !== 80 || fs.statSync('/usr/local/bin').uid !== process.getuid()) {
       return true;
     }
 
-    if (fs.statSync('/usr/local/bin/docker-machine').gid !== 80 || fs.statSync('/usr/local/bin/docker-machine').uid !== process.getuid()) {
+    if (fs.existsSync('/usr/local/bin/docker') && (fs.statSync('/usr/local/bin/docker').gid !== 80 || fs.statSync('/usr/local/bin/docker').uid !== process.getuid())) {
+      return true;
+    }
+
+    if (fs.existsSync('/usr/local/bin/docker-machine') && (fs.statSync('/usr/local/bin/docker-machine').gid !== 80 || fs.statSync('/usr/local/bin/docker-machine').uid !== process.getuid())) {
       return true;
     }
     return false;
@@ -50,9 +50,11 @@ var SetupUtil = {
   },
   fixBinariesCmd: function () {
     var cmd = [];
-    cmd.push.apply(cmd, ['chown', `${process.getuid()}:${80}`, this.escapePath(path.join('/usr/local/bin', 'docker-machine'))]);
+    cmd.push.apply(cmd, ['chown', `${process.getuid()}:${80}`, path.join('/usr/local/bin')]);
     cmd.push('&&');
-    cmd.push.apply(cmd, ['chown', `${process.getuid()}:${80}`, this.escapePath(path.join('/usr/local/bin', 'docker'))]);
+    cmd.push.apply(cmd, ['chown', `${process.getuid()}:${80}`, path.join('/usr/local/bin', 'docker-machine')]);
+    cmd.push('&&');
+    cmd.push.apply(cmd, ['chown', `${process.getuid()}:${80}`, path.join('/usr/local/bin', 'docker')]);
     return cmd.join(' ');
   },
   installVirtualBoxCmd: function () {
diff --git a/util/deps b/util/deps
index 7d7dff31d1..25bbaaf8f3 100755
--- a/util/deps
+++ b/util/deps
@@ -11,7 +11,9 @@ pushd $BASE/resources > /dev/null
 if [ ! -f $DOCKER_MACHINE_CLI_FILE ]; then
   echo "-----> Downloading Docker Machine CLI..."
   rm -rf docker-machine*
-  curl -L -o $DOCKER_MACHINE_CLI_FILE https://github.com/docker/machine/releases/download/v$DOCKER_MACHINE_CLI_VERSION/docker-machine_darwin-amd64
+  # Use temporary, new version of docker-machine that has some important fixes
+  # curl -L -o $DOCKER_MACHINE_CLI_FILE https://github.com/docker/machine/releases/download/v$DOCKER_MACHINE_CLI_VERSION/docker-machine_darwin-amd64
+  curl -L -o $DOCKER_MACHINE_CLI_FILE https://github.com/kitematic/kitematic/releases/download/v0.5.8/docker-machine_darwin-amd64
   chmod +x $DOCKER_MACHINE_CLI_FILE
 fi