This is as-designed. Team Explorer Everywhere can only connect to a single Team Project Collection at a time. There are myriad reasons why this is the case, but all are to preserve the notion of atomic operations against the server. Some operations (for example, check-in) simply must be scoped to a single server instance in order to make sense.
Since a single changeset is atomic in TFS, an attempt to check-in multiple pending changes either all succeed or all fail. Consider if you had pending changes from two different servers: you cannot commit all these changes as a single changeset - one server could reject your check-in due to conflicts, while the other could proceed successfully. This is, at best, confusing, but most likely actually leaves your projects in an inconsistent state since there may be dependencies between these projects. Since there are distinct changesets for each server, the UI must reflect that.
After much deliberation and experimentation, we concluded that the best user experience is simply to have an experience where you can import projects from multiple TFS servers, but you must select which server you want to work with in the UI by selecting which one is currently "online". All TFS functionality is available for the online server which a limited subset of the TFS functionality is available to the other projects.
We would recommend that you consolidate your Java projects to a single Team Project Collection if you need to import all of them.
This behavior is unchanged from any previous versions of the software, including before the acquisition of the technology by Microsoft (when the product was still part of Teamprise Client Suite.)
Also note that the scope of commands available to "offline" projects has increased dramatically in TFS 2012 thanks to the new Local Workspace functionality.