Quick ideas what probably went wrong: you fixed strong name signature (in .NET directory) but forgot to update Assembly table. You forgot to update AssemblyRef table. You did not clean GAC cache. Maybe ASP.NET caches assemblies somehow.
It's hard to tell based on your vague description.
Read ECMA-335 standard, all answers can be found there. Or, if you just want to get the job done, use some of existing tools like ReSign or Strong.name.helper