Reproduced with Inkscape 0.47 and 0.48.x with the file attached in comment #2,
not reproduced with Inkscape 0.48+devel r11503 on OS X 10.7.4
The only "trigger" I was able to detect is the zoom level, likely combined with the relation of the size of the rectangle - which is covering the flowed text object - to the visible canvas area at different zoom levels.
Closing as 'Fix Committed' (milestoned for 0.49) - please reopen if you are able to reproduce it with current trunk (and figure out what exactly triggers this rendering error).
Reproduced with Inkscape 0.47 and 0.48.x with the file attached in comment #2,
not reproduced with Inkscape 0.48+devel r11503 on OS X 10.7.4
The only "trigger" I was able to detect is the zoom level, likely combined with the relation of the size of the rectangle - which is covering the flowed text object - to the visible canvas area at different zoom levels.
Closing as 'Fix Committed' (milestoned for 0.49) - please reopen if you are able to reproduce it with current trunk (and figure out what exactly triggers this rendering error).