Thanks. I believe I found the issue. It seems my custom connection produced this weird artifact when I explicitly set the target cap in its constructor:
public MyChartConnection(Link link)
SourceConnectorPosition = ConnectorPosition.Auto;
TargetConnectorPosition = ConnectorPosition.Auto;
SourceCapType = link.SourceCapType;
TargetCapType = link.TargetCapType;
Could have had something to do with my connector names too. Not sure. I refactored large parts of the code since this issue!