I use FME to change Esri shapefiles to Netezza Spatial all the time, until last night. It is only writing out a fraction of the rows. I don't understand why. I have tried both a polygon shapefile and a line shapefile. The shapefiles are fairly small -- 20-4,000 features with only 2-15 attributes.
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I would suggest that you send a sample of the data, your workspace and the FME log file to you're FME support contact. Either through safe.com/support or your FME reseller. Since the FME behaviour seems to have changed form working to not working, you should also try and document what might have changed on your system to trigger this bad behaviour - an FME upgrade, Netezza table changes.