While I don't know WHY this has failed, I found out that loading and setting the tracking profile via the IIS Management screen didn't work.
When I placed the entire configuration in the web.config
file (tracking profile definition and selecting it as the default tracking profile for our workflows) then it started to work as expected.
Here's the important part of the final web.config
if anyone's interested. :)
<system.serviceModel>
<tracking>
<profiles>
<trackingProfile name="My Tracking Profile" implementationVisibility="All">
<workflow activityDefinitionId="*">
<workflowInstanceQueries>
<workflowInstanceQuery>
<states>
<state name="Started" />
<state name="UnhandledException" />
<state name="Persisted" />
<state name="Unsuspended" />
<state name="Aborted" />
<state name="Canceled" />
<state name="Completed" />
<state name="Terminated" />
</states>
</workflowInstanceQuery>
</workflowInstanceQueries>
<activityStateQueries>
<activityStateQuery activityName="*">
<states>
<state name="Closed" />
</states>
</activityStateQuery>
</activityStateQueries>
<customTrackingQueries>
<customTrackingQuery name="*" activityName="*" />
</customTrackingQueries>
<faultPropagationQueries>
<faultPropagationQuery faultSourceActivityName="*" faultHandlerActivityName="*" />
</faultPropagationQueries>
</workflow>
</trackingProfile>
</profiles>
</tracking>
<bindings />
<client />
<behaviors>
<serviceBehaviors>
<behavior>
<etwTracking profileName="My Tracking Profile"/>
(...)