Well, you may simply have a bad batch of filters and/or dirty reagents. Its unlikely, but still, you have to wonder sometimes.
Is your vacuum source still at its best?
When you transfer the eluent, is the filter now covered with air bubbles? Because the liquid can't get under them, and that's surface area that's not available.
I have taken more than a few hours to filter eleunt, but that's when I was using a filter rig, meant for 500 ml, to filter 2 liters. So maybe just buy a bigger vacuum rig.