QGIS algorithms do not work on copies of shapefiles?

I'm using QGIS 2.6.0. I'm trying to run various algorithms such as "SAGA/Shapes-points/remove duplicates" & "SASA/Shapes-Grid/Add grid values to points" through the sextant toolbox.

When I run these algorithms on a shapefile (initially created via the QGIS option "Create a Layer from a Delimited Text File" and then saving the output as a shapefile), it works fine. However, if I create a copy of the shapefile through QGIS (i.e. using Save As) even with no changes (e.g. same coordinate system) and try to run these algorithms using the same input parameters, it fails. An example of the error that appears is as follows:

"Oooops! The following output layers could not be open Result: C:\Users\stephen\AppData\Local\Temp\processing\bf494593f4a44905bb4ec0bbe0a7f847\RESULT.shp The above files could not be opened, which probably indicates that they were not correctly produced by the executed algorithm Checking the log information might help you see why those layers were not created as expected This algorithm requires SAGA to be run. A test to check if SAGA is correctly installed and configured in your system has been performed, with the following result: SAGA seems to be correctly installed and configured"

The log output is as follows:

"SAGA execution console output

C:\PROGRA~1\QGISBR~1\bin>set SAGA=C:/PROGRA~1/QGISBR~1/apps\saga

C:\PROGRA~1\QGISBR~1\bin>set SAGA_MLB=C:/PROGRA~1/QGISBR~1/apps\saga\modules

C:\PROGRA~1\QGISBR~1\bin>PATH=PATH;C:/PROGRA~1/QGISBR~1/apps\saga;C:/PROGRA~1/QGISBR~1/apps\saga\modules

C:\PROGRA~1\QGISBR~1\bin>saga_cmd shapes_points "Remove Duplicate Points" -POINTS "E:/Studies/Data/Consolidated/Records_06092014_Copy.shp" -FIELD "Precision" -METHOD 0 -NUMERIC 1 -RESULT "C:\Users\stephen\AppData\Local\Temp\processing\bf494593f4a44905bb4ec0bbe0a7f847\RESULT.shp"

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library path: C:/PROGRA~1/QGISBR~1/apps\saga\modules library name: shapes_points module name : Remove Duplicate Points author : O.Conrad (c) 2008

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go...

Load shapes: E:/Studies/Data/Consolidated/Records_06092014_Copy.shp...

ready

okay

Remove Duplicate Points: Invalid parameters!

Shapes: Points

error: executing module [Remove Duplicate Points]

C:\PROGRA~1\QGISBR~1\bin>exit"

Just wondering whether anyone has come across a similar problem and if they have found a solution?

Thanks kindly, Stephen.