diff --git a/OfflineMerge/OfflineMerge.cs b/OfflineMerge/OfflineMerge.cs
index e7d417ff..70ef2594 100644
--- a/OfflineMerge/OfflineMerge.cs
+++ b/OfflineMerge/OfflineMerge.cs
@@ -172,18 +172,19 @@ namespace SabreTools
 			Dictionary<string, List<RomData>> netNew = new Dictionary<string, List<RomData>>();
 			foreach (string key in completeDats.Keys)
 			{
-				if (completeDats[key].Count == 1)
+				List<RomData> templist = RomManipulation.Merge(completeDats[key]);
+				foreach (RomData rom in templist)
 				{
-					if (completeDats[key][0].System == _currentNewMerged)
+					if (!rom.Dupe && rom.System == _currentNewMerged)
 					{
 						if (netNew.ContainsKey(key))
 						{
-							netNew[key].Add(completeDats[key][0]);
+							netNew[key].Add(rom);
 						}
 						else
 						{
 							List<RomData> temp = new List<RomData>();
-							temp.Add(completeDats[key][0]);
+							temp.Add(rom);
 							netNew.Add(key, temp);
 						}
 					}
@@ -195,18 +196,19 @@ namespace SabreTools
 			Dictionary<string, List<RomData>> unneeded = new Dictionary<string, List<RomData>>();
 			foreach (string key in completeDats.Keys)
 			{
-				if (completeDats[key].Count == 1)
+				List<RomData> templist = RomManipulation.Merge(completeDats[key]);
+				foreach (RomData rom in templist)
 				{
-					if (completeDats[key][0].System == _currentAllMerged)
+					if (!rom.Dupe && rom.System == _currentAllMerged)
 					{
 						if (unneeded.ContainsKey(key))
 						{
-							unneeded[key].Add(completeDats[key][0]);
+							unneeded[key].Add(rom);
 						}
 						else
 						{
 							List<RomData> temp = new List<RomData>();
-							temp.Add(completeDats[key][0]);
+							temp.Add(rom);
 							unneeded.Add(key, temp);
 						}
 					}
@@ -231,18 +233,19 @@ namespace SabreTools
 			Dictionary<string, List<RomData>> newMissing = new Dictionary<string, List<RomData>>();
 			foreach (string key in midMissing.Keys)
 			{
-				if (midMissing[key].Count == 1)
+				List<RomData> templist = RomManipulation.Merge(midMissing[key]);
+				foreach (RomData rom in templist)
 				{
-					if (midMissing[key][0].System == _currentMissingMerged)
+					if (!rom.Dupe && rom.System == _currentMissingMerged)
 					{
 						if (newMissing.ContainsKey(key))
 						{
-							newMissing[key].Add(midMissing[key][0]);
+							newMissing[key].Add(rom);
 						}
 						else
 						{
 							List<RomData> temp = new List<RomData>();
-							temp.Add(midMissing[key][0]);
+							temp.Add(rom);
 							newMissing.Add(key, temp);
 						}
 					}
@@ -302,18 +305,19 @@ namespace SabreTools
 			Dictionary<string, List<RomData>> have = new Dictionary<string, List<RomData>>();
 			foreach (string key in midHave.Keys)
 			{
-				if (midHave[key].Count == 1)
+				List<RomData> templist = RomManipulation.Merge(midHave[key]);
+				foreach (RomData rom in templist)
 				{
-					if (midHave[key][0].System == _currentNewMerged)
+					if (!rom.Dupe && rom.System == _currentNewMerged)
 					{
 						if (have.ContainsKey(key))
 						{
-							have[key].Add(midHave[key][0]);
+							have[key].Add(rom);
 						}
 						else
 						{
 							List<RomData> temp = new List<RomData>();
-							temp.Add(midHave[key][0]);
+							temp.Add(rom);
 							have.Add(key, temp);
 						}
 					}
diff --git a/SabreHelper/Output.cs b/SabreHelper/Output.cs
index 61caf02e..4f4a62de 100644
--- a/SabreHelper/Output.cs
+++ b/SabreHelper/Output.cs
@@ -154,7 +154,13 @@ namespace SabreTools.Helper
 			long count = 0;
 			foreach (List<RomData> roms in dict.Values)
 			{
-				foreach (RomData rom in roms)
+				List<RomData> newroms = roms;
+				if (merge)
+				{
+					newroms = RomManipulation.Merge(newroms);
+				}
+
+				foreach (RomData rom in newroms)
 				{
 					count++;
 					string key = rom.SystemID + "-" + rom.SourceID + "-" + rom.Game + "-" + rom.Name;
@@ -168,11 +174,6 @@ namespace SabreTools.Helper
 						temp.Add(rom);
 						sortable.Add(key, temp);
 					}
-
-					if (merge)
-					{
-						break;
-					}
 				}
 			}
 
diff --git a/SabreHelper/RomManipulation.cs b/SabreHelper/RomManipulation.cs
index d1e89a1a..b91ef840 100644
--- a/SabreHelper/RomManipulation.cs
+++ b/SabreHelper/RomManipulation.cs
@@ -467,7 +467,7 @@ namespace SabreTools.Helper
 											sha1 = (sha1.StartsWith("0x") ? sha1.Remove(0, 2) : sha1);
 
 											// Get the new values to add
-											string key = crc + "-" + md5 + "-" + sha1 + "-" + size;
+											string key = crc + "-" + size;
 											RomData value = new RomData
 											{
 												Game = tempname,
@@ -590,6 +590,7 @@ namespace SabreTools.Helper
 						last.CRC = (last.CRC == "" && rom.CRC != "" ? rom.CRC : last.CRC);
 						last.MD5 = (last.MD5 == "" && rom.MD5 != "" ? rom.MD5 : last.MD5);
 						last.SHA1 = (last.SHA1 == "" && rom.SHA1 != "" ? rom.SHA1 : last.SHA1);
+						last.Dupe = true;
 
 						outroms.RemoveAt(outroms.Count - 1);
 						outroms.Insert(outroms.Count, last);
@@ -611,7 +612,6 @@ namespace SabreTools.Helper
 			return outroms;
 		}
 
-
 		/// <summary>
 		/// Sort a list of RomData objects by SystemID, SourceID, Game, and Name (in order)
 		/// </summary>
diff --git a/SabreHelper/Structs.cs b/SabreHelper/Structs.cs
index 875d89f8..7e2647bf 100644
--- a/SabreHelper/Structs.cs
+++ b/SabreHelper/Structs.cs
@@ -18,5 +18,6 @@
 		public string CRC;
 		public string MD5;
 		public string SHA1;
+		public bool Dupe;
 	}
 }