I may be mistaken, but it seems to me that Eclipse may not see your imported TFS projects as Java projects (Eclipse also supports "simple" projects, among others). When you look at * .java files in the package hierarchy of your projects, do they have blue "J" in the corresponding icons or are they "hollow"?
If the first is true, then Eclipse will see your projects as Java projects, I will be completely confused, and you can ignore my answer;)
If the latter is true, then the project is not configured as a "Java project". This may be a real obstacle to a solution ... but one solution in this case could be to rename your existing projects to something else (for example, MainProjectOld, SecondProjectOld), create new projects "MainProject" and "SystemProject" as new " Java "projects, then copy all the source code from the old to the new source folders. I don't know much about TeamFoundationServer, but I would suggest that at this point you can reconnect your new projects to TFS and validate them as Java projects.
EDIT
The bottom line contains, if the latter is true, then it looks like the project configuration XML files do not get into TFS, and Eclipse gets confused with how it should handle projects (simple, Java or others) after the initial import from TFS. I also saw this in CVS and SVN, so I assume this is a fairly common problem in any version control system supported by Eclipse. TFS can be included in this group.
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