The problems I've had are always when sentences in the target language compared to sentences in the translation don't line up. It's not always obvious where the sentences are split up, either, like when a sentence has quotes or other things that LingQ considers the end of a sentence.

Try going into the lesson editor and count the number of sentences, and make sure you have the exact same number. If they're off, you can scroll through the lesson and check to see where the translated text went off the rails, then modify the translation accordingly. You can just copy-paste the translation again and iterate until it all matches.

Hope this is making sense... If not, can you describe how you are trying to sync it up?

Can you please give us more information on the issue? What exactly doesn't work for you?