It sounds like CRM may be having a problem loading your assembly, or confusing it for an older version of the same assembly.
Are you versioning your workflow assembly while you develop and deploy it, and is the assembly signed with a strong-name key?
In Visual Studio on the Project tab, make sure you increment the Build/Revision number. See this article: http://gonzaloruizcrm.blogspot.com/2011/08/assembly-versioning-in-crm-2011.html
If you don't increment the Build/Revision, CRM may not see your updated assembly as an "update" and may be trying to use an older, cached version, which can cause all kinds of problems.
You may also try unregistering the assembly completely and then registering your latest version. You might need to update your workflows as well.