There are times when due to different reasons (among which are instance configuration changes) Enterprise Portal or Workflow start to behave strange or not work at all ...
Things to check when this happens:
1. Check the AOS is running ok and that a client can connect to it;
2. Check there is no connectivity issue between the AOS machine and the IIS machine hosting the sites;
3. Check the account used for the BC Proxy in AX (done in Administration -> Setup -> Security -> System service accounts);
4. Check the application pool for the sites that is using the BC Proxy account; also, depending on the IIS version / machine, for AX 2009 make sure you are running a Classic app pool (set on 32 bit for Workflows), you have the correct ASP version, .Net framework version (2.0) and the handlers are setup ok. There is another story for AX 2012.
5. Check the configuration that the EP / Workflow is using. This is the Business Connector configuration in case you are only hosting one instance. If you have multiple instances you should have the web.config pointing to the right .axc file.