we're aware of this "glitch". This behavior is caused by the inner crash-restoration system. New instance found non-closed inner database so it displayed this dialog.
To fix this issue, it will be necessary to rework the inner system for application state for multiple processes. But such rework can introduce a lot of new bugs and ambiguous states (ie. how to decide which of several states are active instances and which are crashed, how to restore app when multiple states are found, etc.).
Because of that, we decided to keep things simple. Because Skipper allows to open multiple projects in one instance this should not be a big deal.
On the other side, we don't want to restrict application to single-instance only because there is no real reason for this except this dialog ;-).