A pattern with a clipped object becomes partly or totally invisible, depending on zoom level and/or if it's selected, in latest inkscape build. (I used http://inkscape.modevia.com/win32/Inkscape19816-0809080916.7z )

The file "mesh7_046R" contains a pattern = (objects + a clipped rectangle) and was not opened with later builds of Inkscape. The pattern shows correctly at every zoom level in the 0.46 release..

The file "clipped_pattern046R_046Dev" is the same (mesh7_046R), then it was opened in the latest build, and a new similar clipped pattern was created.
Both patterns disappear, totally or partially, depending on whether they are selected or not and on the zoom level.

This seems to only happen to patterns with clipped objects.