We are using Aspose.Word to convert MS Word documents to PDF. Here is the pseudo code for the same -
Aspose.Words.Document doc = new Aspose.Words.Document(sourceFilePath);
Here we are seeing that the shapes and text boxes are getting overlapped in converted PDF. We are using 184.108.40.206 version of Aspose.Word.
I have attached the source and target PDF with this post for more information.
Also, we have priority support of Aspose just in case if required.