Add Tweaker which will ensure transformer is last, if possible.

src/main/java/me/nallar/modpatcher/LaunchClassLoaderUtil.java

@@ -45,7 +45,12 @@ public static void addTransformer(IClassTransformer transformer) {
 
 		int target = -1;
 		for (int i = 0; i < transformers.size(); i++) {
-			String className = transformers.get(i).getClass().getName();
+			IClassTransformer current = transformers.get(i);
+
+			if (current == transformer)
+				transformers.remove(i--);
+
+			String className = current.getClass().getName();
 			if (DEOBF_TRANSFORMER_NAMES.contains(className))
 				target = i;
 		}

src/main/java/me/nallar/modpatcher/ModPatcherTransformer.java

@@ -106,6 +106,7 @@ public static void initialiseClassLoader(LaunchClassLoader classLoader) {
 		classLoader.addTransformerExclusion("com.github.javaparser.");
 
 		LaunchClassLoaderUtil.instance = classLoader;
+		ModPatcherTweaker.add();
 		LaunchClassLoaderUtil.addTransformer(ModPatcherTransformer.getInstance());
 		LaunchClassLoaderUtil.dumpTransformersIfEnabled();
 		LaunchClassLoaderUtil.removeRedundantExclusions();

src/main/java/me/nallar/modpatcher/ModPatcherTweaker.java

@@ -0,0 +1,45 @@
+package me.nallar.modpatcher;
+
+import net.minecraft.launchwrapper.ITweaker;
+import net.minecraft.launchwrapper.Launch;
+import net.minecraft.launchwrapper.LaunchClassLoader;
+
+import java.io.*;
+import java.util.*;
+
+/**
+ * Tries to ensure that our transformer is last
+ */
+public class ModPatcherTweaker implements ITweaker {
+	@SuppressWarnings("unchecked")
+	public static void add() {
+		List<String> newTweaks = (List<String>) Launch.blackboard.get("TweakClasses");
+		newTweaks.add(ModPatcherTweaker.class.getName());
+	}
+
+	private static void inject() {
+		LaunchClassLoaderUtil.addTransformer(ModPatcherTransformer.getInstance());
+	}
+
+	@Override
+	public void acceptOptions(List<String> list, File file, File file1, String s) {
+		inject();
+	}
+
+	@Override
+	public void injectIntoClassLoader(LaunchClassLoader launchClassLoader) {
+		inject();
+	}
+
+	@Override
+	public String getLaunchTarget() {
+		inject();
+		return null;
+	}
+
+	@Override
+	public String[] getLaunchArguments() {
+		inject();
+		return new String[0];
+	}
+}