R – Sharepoint workflow remains “in progress” despite all actions being complete

I think you already read Chris O'brien's comments on this topic. so here is the second link : http://msmvps.com/blogs/theproblemsolver/archive/2008/09/10/versioning-long-running-workfows.aspx

Try attaching a debugger to the SPTimer service -this is responsible for running workflow code asynchronously - this might give you some hints. Also ensure that the account running sptimer has not gotten out of sync with the farm account, in terms of credentials (password expired etc). Don't forget to bounce this service too when updating your workflow builds - bouncing IIS is not enough. The timer service may have the workflow assembly loaded.

-Oisin