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It seems that's this problem isn't resolved at all. I have it too...
The query is like this : "Select Id, CustomField__c FROM Account Where CustomField__c !=null"
The number of lines is correct, the query works perfectly with the application Force.com but with Talend, the field CustomField__c is always Null.
I've found on https://help.talend.com/reader/_YDfvfhmdBzbX9dWMenklg/Lv~Pqm4u2XWOeTfUjL1xMA that there are tSalesforceInput Limitations when "the field with the underscore character '_' in its name"
But what can I do have the values, then ?
Introduction to Talend Open Studio for Data Integration.
Practical steps to developing your data integration strategy.
Create systems and workflow to manage clean data ingestion and data transformation.