Once the instances are created the system programaticly goes through all bookmarks in the document then when its finished the instance is made visible. and the user is able to edit the document and close it themselves, you raised a good point but one that I can say for certain is not the problem, also it would not explain the issues with the same problem with the database where closing the database yields the same result with an instance still running in the back ground.
I have had this same problem running office apllications completly seperatly from our database. Some times they just don't seem to close properly.... Excell, word and access all apear to do this.