diff --git a/.appveyor.yml b/.appveyor.yml
index 4800e33c2..c822f2293 100644
--- a/.appveyor.yml
+++ b/.appveyor.yml
@@ -27,3 +27,4 @@ test_script:
   - test.bat
   - test1.bat
   - test2.bat
+  - test3/test3.bat
diff --git a/citest/test3/.jvmopts b/citest/test3/.jvmopts
new file mode 100644
index 000000000..ecacefc9a
--- /dev/null
+++ b/citest/test3/.jvmopts
@@ -0,0 +1,3 @@
+-XX:+CMSClassUnloadingEnabled
+#-XX:ReservedCodeCacheSize=192m
+#-Duser.timezone=GMT
\ No newline at end of file
diff --git a/citest/test3/build.sbt b/citest/test3/build.sbt
new file mode 100644
index 000000000..3ff4eae20
--- /dev/null
+++ b/citest/test3/build.sbt
@@ -0,0 +1,24 @@
+lazy val check = taskKey[Unit]("")
+
+lazy val root = (project in file("."))
+  .settings(
+    scalaVersion := "2.12.4",
+    name := "Hello",
+    check := {
+      val xs = IO.readLines(file("output.txt")).toVector
+
+      println(xs)
+
+      assert(xs(0) startsWith "[info] Loading project definition")
+      assert(xs(1) startsWith "[info] Loading settings from build.sbt")
+      assert(xs(2) startsWith "[info] Set current project to Hello")
+      assert(xs(3) startsWith "[info] This is sbt")
+      assert(xs(4) startsWith "[info] The current project")
+      assert(xs(5) startsWith "[info] The current project is built against Scala 2.12.4")
+
+      val ys = IO.readLines(file("err.txt")).toVector.distinct
+
+      assert(ys.size == 1, s"ys has more than one item: $ys")
+      assert(ys(0) startsWith "Java HotSpot(TM) 64-Bit Server VM warning")
+    }
+  )
diff --git a/citest/test3/test3.bat b/citest/test3/test3.bat
new file mode 100644
index 000000000..8b3fe5a94
--- /dev/null
+++ b/citest/test3/test3.bat
@@ -0,0 +1,17 @@
+@echo on
+
+SETLOCAL
+
+SET JAVA_HOME=C:\jdk9
+SET PATH=C:\jdk9\bin;%PATH%
+SET SBT_OPTS=-Xmx4g -Dfile.encoding=UTF8
+
+SET BASE_DIR=%CD%
+SET SCRIPT_DIR=%~dp0
+
+CD %SCRIPT_DIR%
+"%BASE_DIR%freshly-baked\sbt\bin\sbt" about 1> output.txt 2> err.txt
+"%BASE_DIR%freshly-baked\sbt\bin\sbt" check
+CD %BASE_DIR%
+
+ENDLOCAL
diff --git a/src/universal/bin/sbt.bat b/src/universal/bin/sbt.bat
index 4e966daac..237accc05 100644
--- a/src/universal/bin/sbt.bat
+++ b/src/universal/bin/sbt.bat
@@ -35,9 +35,11 @@ IF DEFINED JAVA_HOME SET "PATH=%JAVA_HOME%\bin;%PATH%"
 
 rem users can set JAVA_OPTS via .jvmopts (sbt-extras style)
 IF EXIST .jvmopts FOR /F %%A IN (.jvmopts) DO (
-  SET JAVA_OPTS=%%A !JAVA_OPTS!
+  SET _jvmopts_line=%%A
+  IF NOT "!_jvmopts_line:~0,1!"=="#" (
+    SET JAVA_OPTS=%%A !JAVA_OPTS!
+  )
 )
-
 rem We use the value of the JAVACMD environment variable if defined
 set _JAVACMD=%JAVACMD%