Just an FYI, I tested something similar to make sure there isn't a defect in the product, and I was able to get a simple test to work. I created a rudimentary Workflow project with a few Dialog Workflow components, and published it to IIS as a webservice. Then I called that webservice, using a Web Service Caller Generator, from a simple WebForms project. The WebForms project did successfully call the Workflow via the webservice, and I was able to use the returned WorkflowTrackingID to hit services such as TrackStatus and a few others that I tried.
I'm not sure what may be wrong with your project. Are you positive that the Workflow is staying active long enough for you to determine if it is running? When you run the Workflow project in the debugger, how long does it stay active? If it's just processing some data and ending, it may only stay "alive" for a few seconds, which isn't long enough for you to use the WorkflowManagementService to query it.