Has the systemadmin account be parrte of every group in other to have access to all? We have some permissions schemes based on groups, so if the systemadmin account is not part of these groups, would that mean that sysadmin will not be able to access issues within a project that has certain permission schemes?
System admin rights give you system administration rights. That's it. (Admin can see/do everything automatically is a dreadful access model for all sorts of reasons and one that Atlassian have rightly stayed away from)
If you want access to a project, you need to grant yourself project rights.
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