Stick this in an Editor folder in your project. Every time the solution file is recreated by Unity it will remove all the cruft that Unity injects into the file. Hopefully, one day, Unity will actually fix this on their end.

StripGeneratedSolutionSettings

/*

v2: Matt Rix pointed out there's an undocumented ONGeneratedCSProjectFiles() callback
https://gist.github.com/MattRix/0bf8de88e16e8b494dbb

v1: Still available in the gist history if you want a FileSystemWatcher solution!

THE PROBLEM:

- Unity constantly rewrites its .sln files whenever you rename/add/remove scripts
- Their solution files includes a bunch of formatting/tab/etc settings
- Unfortunately, MonoDevelop / Xamarin Studio give these settings priority over your other defaults

(At least sometimes--over here I only get issues maybe once or twice a day)

THE SOLUTION:

- Strip out this entire block of settings whenever any .sln file changes

TO USE:

- Toss this script anywhere in an Editor/ folder
- Enjoy your tabs not getting constantly mangled!

Enjoy,
Matthew / Team Colorblind

*/


using UnityEngine;
using UnityEditor;
using System.IO;
using System.Text.RegularExpressions;



public class StripGeneratedSolutionSettings : AssetPostprocessor
{
	/// <summary>
	/// Undocumented callback, thanks Matt Rix!
	/// </summary>
	private static void OnGeneratedCSProjectFiles()
	{
		var currentDir = Directory.GetCurrentDirectory();
		foreach( var filePath in Directory.GetFiles( currentDir, "*.sln" ) )
			fixSolution( filePath );

		foreach( var filePath in Directory.GetFiles( currentDir, "*.csproj" ) )
			fixProject( filePath );
	}


	/// <summary>
	/// Put any project changes here
	/// </summary>
	/// <returns><c>true</c>, if project was fixed, <c>false</c> otherwise.</returns>
	/// <param name="filePath">File path.</param>
	static void fixProject( string filePath )
	{
		var content = File.ReadAllText( filePath );

		var searchString = "<TargetFrameworkVersion>v3.5</TargetFrameworkVersion>";
		var replaceString = "<TargetFrameworkVersion>v4.0</TargetFrameworkVersion>";

		if( content.IndexOf( searchString ) != -1 )
		{
			content = Regex.Replace( content, searchString, replaceString );
			File.WriteAllText( filePath, content );
		}
	}


	/// <summary>
	/// Remove settings and .unityproj files
	/// </summary>
	/// <returns><c>true</c>, if solution was fixed, <c>false</c> otherwise.</returns>
	/// <param name="filePath">File path.</param>
	static void fixSolution( string filePath )
	{
		var content = File.ReadAllText( filePath );
		var newContent = content;

		// xamarin studio/monodevelop barf on .unityproj files
		var stripUnityProject = @"Project.*?EndProject";
		newContent = Regex.Replace( newContent, stripUnityProject, cleanProjects, RegexOptions.Singleline );

		// strip out all solution preferences
		var stripSettings = @"GlobalSection\(MonoDevelopProperties\)\s=\spreSolution.*EndGlobalSection";
		newContent = Regex.Replace( newContent, stripSettings, "", RegexOptions.Singleline | RegexOptions.RightToLeft );

		// save back if it was changed
		if( content != newContent )
			File.WriteAllText( filePath, newContent );
	}


	/// <summary>
	/// If our project match is a .unityproj file, strip it
	/// </summary>
	/// <returns>The projects.</returns>
	/// <param name="m">M.</param>
	static string cleanProjects( Match m )
	{
		string text = m.ToString();

		if( text.Contains( ".unityproj" ) )
			return "";
		else
			return text;
	}
}

With the new "MonoDevelop Solution Properties" option added in patch 5.1.0P1, is this still required?