It seems Mylar confuses the Package Explorer's Filter settings.
It seems to affect mostly the "Hide .pyc files". Although it is activated, the files are not hidden when klicking the "Focus on active Task" button, or using alt-click to show Mylar-hidden files of a project.
Pydev Mylar Integration 0.2.0
I noticed also a strange behaviour when the Mylar Context filter is active: when I use Alt-Click to show the hidden items to open another file, some of the already open files lost their landmark status and were removed from the explorer and another file (a unused one) took its place (but only in the label, when I clicked it it opened the correct file)