If you are using WinMerge 2.14.0 I recommend you use the older 2011 version instead (change the .7z file extension to .exe to install it).
If I compare two folders in WinMerge 2.14.0 and then sort on the 'Comparison result' column, it does not sort the column correctly. This means that some files which are 'Left only' are not sorted to the top or bottom and so if you have a lot of files, you will miss the 'Left only' files as they appear further down the listing and are mixed in with 'Right only' entries! This is a serious bug and so I recommend you to use the 2011 version instead.
P.S. I had this issue on two different Win7 64-bit systems. It seems to depend on which folder you have on the Left and which one is on the Right. If I simply swap over the two folders, then it works correctly (i.e. Left=folderX v. Right=folderY = WORKS OK, Left=folderY v. Right=folderX = DOES NOT SORT CORRECTLY!
If I compare two folders in WinMerge 2.14.0 and then sort on the 'Comparison result' column, it does not sort the column correctly. This means that some files which are 'Left only' are not sorted to the top or bottom and so if you have a lot of files, you will miss the 'Left only' files as they appear further down the listing and are mixed in with 'Right only' entries! This is a serious bug and so I recommend you to use the 2011 version instead.
P.S. I had this issue on two different Win7 64-bit systems. It seems to depend on which folder you have on the Left and which one is on the Right. If I simply swap over the two folders, then it works correctly (i.e. Left=folderX v. Right=folderY = WORKS OK, Left=folderY v. Right=folderX = DOES NOT SORT CORRECTLY!
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