Are you going nuts after deploying your workflows & several IISRESETs and you see that it still behaves the same???
If your changes were on the designer editor (for instance changing a method for a if branch condition). After deploying your solution (or manually copying your DLL to the GAC) you need:
1. Remove the workflow from the list that uses it
2. Deactivate the Feature of the workflow
3. Reactivate the feature.
4. Re-attach the workflow to the list.