Media encoder not syncing audio properly

Never had this happen before but when i go to export media and do my settings as normal then go to queue, the audio from prem pro cs6 timeline is for some reason syncing a part of the audio from the start of the wedding and not from the timeline project sequence. Its as if its syncing the part when i put the voice recorder on the groom early on in the morning and not the vows i want in the timeline. It was synced with pluraleyes. The only thing i see in the timeline is the green synced sequence says audio drift corrected, any thing wrong there? Steve uk