Didnt test it fully, but it seem to work.

0001-fixed-idea-task-module-configuration.patch

From 61b82b19fc1db023105041534128ef6561ce3fb8 Mon Sep 17 00:00:00 2001
From: xalcon <xalcon@xalcon.net>
Date: Wed, 28 Jun 2017 17:26:21 +0200
Subject: [PATCH] fixed idea task module configuration

---
 src/main/java/net/minecraftforge/gradle/user/UserBasePlugin.java | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/main/java/net/minecraftforge/gradle/user/UserBasePlugin.java b/src/main/java/net/minecraftforge/gradle/user/UserBasePlugin.java
index 1a025ad..9a0ce18 100644
--- a/src/main/java/net/minecraftforge/gradle/user/UserBasePlugin.java
+++ b/src/main/java/net/minecraftforge/gradle/user/UserBasePlugin.java
@@ -1137,7 +1137,7 @@ public abstract class UserBasePlugin<T extends UserBaseExtension> extends BasePl
             {
                 try
                 {
-                    String module = task.getProject().getProjectDir().getCanonicalPath();
+                    String module = ((IdeaModel)task.getProject().getExtensions().getByName("idea")).getModule().getName() + "_" + getExtension().getRunSourceSet().getName();
 
                     File root = task.getProject().getProjectDir().getCanonicalFile();
                     File file = null;
@@ -1205,7 +1205,7 @@ public abstract class UserBasePlugin<T extends UserBaseExtension> extends BasePl
                 Document doc = root.getOwnerDocument();
                 try
                 {
-                    injectIntellijRuns(doc, project.getProjectDir().getCanonicalPath());
+                    injectIntellijRuns(doc, ((IdeaModel) project.getExtensions().getByName("idea")).getModule().getName());
                 }
                 catch (Exception e)
                 {
@@ -1280,7 +1280,7 @@ public abstract class UserBasePlugin<T extends UserBaseExtension> extends BasePl
             addXml(child, "option", ImmutableMap.of("name", "ENABLE_SWING_INSPECTOR", "value", "false"));
             addXml(child, "option", ImmutableMap.of("name", "ENV_VARIABLES"));
             addXml(child, "option", ImmutableMap.of("name", "PASS_PARENT_ENVS", "value", "true"));
-            addXml(child, "module", ImmutableMap.of("name", ((IdeaModel) project.getExtensions().getByName("idea")).getModule().getName() + '_' + getExtension().getRunSourceSet().getName()));
+            addXml(child, "module", ImmutableMap.of("name", module));
             addXml(child, "RunnerSettings", ImmutableMap.of("RunnerId", "Run"));
             addXml(child, "ConfigurationWrapper", ImmutableMap.of("RunnerId", "Run"));
         }
-- 
2.12.2.windows.1