Steven,
Git works just fine in MyEclipse – there isn’t any team functionality that we interfere with or modify and the eGit plugins are not managed by us.
1) I would check that you are using the same version of eGit with both Juno and MyEclipse.
2) Additionally, all I can think of is that you are experiencing actual Git issues due to repository misconfiguration or just incorrect Git handling.
For instance, the case where you pushed new files and another person pulled them and found them marked new; even if MyEclipse modified the files, they would be marked as unstaged changes, not new files. Furthermore the responsibility of decorating them with the question mark falls on eGit, not MyEclipse (we have no reason to mess with team decorators) Perhaps he did a mixed reset to an earlier commit? I’m not saying that this is the issue, we are using Git ourselves and I know there are, unfortunately, several things that can go wrong, most of these being user errors.
I hope this helps, please let us know if you have further questions.