I have installed squishit version 0.9.8.2 with Ajaxmin 4.96.4941. The problem is that when I run the ASP.net site I get error
[FileLoadException: Could not load file or assembly 'AjaxMin, Version=4.48.4489.28432, Culture=neutral, PublicKeyToken=21ef50ce11b5d80f' or one of its dependencies. The located assembly's manifest definition does not match the assembly reference. (Exception from HRESULT: 0x80131040)]
SquishIt.Framework.Minifiers.JavaScript.MsMinifier.Minify(String content) in c:\dev\urandom\SquishIt\SquishIt.Framework\Minifiers\JavaScript\MsMinifier.cs:31
SquishIt.Framework.Base.BundleBase1.MinifyIfNeeded(String content, Boolean minify) in c:\dev\urandom\SquishIt\SquishIt.Framework\Base\BundleBase.Rendering.Internals.cs:340
System.Linq.WhereSelectArrayIterator2.MoveNext() +110
System.Linq.d__162.MoveNext() +348
System.Collections.Generic.List1..ctor(IEnumerable1 collection) +476
System.Linq.Enumerable.ToList(IEnumerable1 source) +69
SquishIt.Framework.JavaScript.JavaScriptBundle.AggregateContent(List1 assets, StringBuilder sb, String outputFile) in c:\dev\urandom\SquishIt\SquishIt.Framework\JavaScript\JavaScriptBundle.cs:84
SquishIt.Framework.Base.BundleBase1.GetMinifiedContent(List1 assets, String outputFile) in c:\dev\urandom\SquishIt\SquishIt.Framework\Base\BundleBase.Rendering.Internals.cs:333
SquishIt.Framework.Base.BundleBase1.RenderRelease(String key, String renderTo, IRenderer renderer) in c:\dev\urandom\SquishIt\SquishIt.Framework\Base\BundleBase.Rendering.Internals.cs:290
I think there was a problem with 4.96 at some point but don't remember exactly what. Have you tried adding a binding redirect?
I'd recommend updating to 4.97.4951.28483 (or using the YUI minifier).
For the latter, somewhere in global.asax.cs (before you do any bundle rendering)
Bundle.ConfigureDefaults().UseYuiForJsMinification()