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Qgis 2.8, gdal python scripts gives error at end of process

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I am using Qgis 2.8.1 64-bit (Standalone installer) which also packages a number or other applications, like OSGeo4W Shell, Saga GIS et.c.

In the OSGeo4W Shell I am encountering a problem with some gdal/ogr python scripts that seem identical to what is described here in another question: link

The problem seems to be restricted to gdal2tiles and gdal_calc, I have done some quick testing and the problem doesn’t seem to exist for other scripts.

What causes this error and how can it be resolved?

System information:
Path in OSGeo4W Shell:
C:PROGRA~1QGISWI~1appsPython27Scripts;C:PROGRA~1QGISWI~1bin;C:Windowssystem32;C:Windows;C:WindowsWBem;
C:PROGRA~1QGISWI~1appsmsysbin

pythonhome:
C:PROGRA~1QGISWI~1appsPython27

gdal_data:
C:PROGRA~1QGISWI~1sharegdal


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