I have a student using EndNote X6 with word 2010 and APA 6th. When an in text citation is added to Word nothing appears in the document no reference list appears either. If you use alt F9 the reference coding appears and if you unformatted the document the reference appears inside {} in the correct format. I have checked that all the EndNote addins are active and also that his Word program allows macros. Is there any other setting I should look at. Both the EndNote and the Word style say it is using APA 6th.
Are you sure that the document itself is using APA 6th? It sounds like it may be using an output style that depends on Footnotes?
Try switching to another output style – Like Numbered or Annotated? do the citations now get numbered, for numbered or (author,year) for annotatedand a list of references appear at the end?
Then try switching the word document output style back to APA 6th? You might also want to download a new version of APA 6th from the Endnote: help dropdown, webstyles finder, incase it got corrupted somehow?