Hi, I recently had to restructure a document and had to copy and paste large sections with citations. The citations ended up in the wrong places! When I fixed them (moved them manually), it reverted back again to the wrong places. Consistently! I work on Mac X5 with Windows 2011.
Have you tried to unformat the citations before copy and pasting? This may help.
Tools → EndNote X5 → Convert to unformatted citations
Format the manuscript again after pasting.