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I have noticed the same problem in our OJS installtion. The problem only seems to exist when I’m logged in as a user, which is registered in several journals. When I’m registered in just one journal the link refers to the journal’s submission page. But I also believe this is at least a usability problem and the link at the journal logo in the backend should always go the journal’s submission page, not to the homepage of the OJS site frontend.

I have made a change in the template
/ojs/lib/pkp/templates/common/header.tpl

Old code

{if $currentContext && $multipleContexts}
        {capture assign=homeUrl}{url journal="index" router=$smarty.const.ROUTE_PAGE}{/capture}
{else}
        {capture assign=homeUrl}{url page="index" router=$smarty.const.ROUTE_PAGE}{/capture}
{/if}

New code

{if $currentContext && $multipleContexts}
    {capture assign=homeUrl}{url page="index" router=$smarty.const.ROUTE_PAGE}{/capture}
{/if}

Now the link always refers to the journal’s frontend homepage.

In the frontend there’s a similiar problem I have mentioned here Link at Page Header Logo Image refers sometimes to Site, sometimes to Journal