The hard-coded filters (all, open, resolved, mine) in the issues list pre-date custom views and, as you've seen, don't work very well with them. All these menu items do is strip off the URL parameters and add hard-coded filter and sort parameters. They don't change the default view, so any default view filter will still get applied (just as it does when filtering and sorting the grid directly). We've talked about switching these filters to actual pre-defined custom views, which might more understandable.

Another thing to note: that issues webpart is not very useful. We could revamp it (e.g., put appropriate links on each open & resolved count), but we haven't bothered since using custom query grids is so much more powerful. As an example, see the issues "dashboard" we use on labkey.org: https://www.labkey.org/project/home/Developer/issues/Reports/begin.view. This works because we don't apply a filter in the default view of our issues list. Let me know if you want to see the LabKey SQL or meta data underlying this dashboard.

Adam