There is a major difference with the way the overlay pages are handled between the Overlay tool from PDFBox 1.6.x and the latest OverlayPDF in 1.8.6.
In the original version, when using a multi-page PDF overlay, all pages from the overlay would be combined with the original document. The latest version only uses the first page of the overlay.
Example with a 6 page document and a 2 page (A, B) overlay:
A, B, A, B, A, B
A, A, A, A, A, A
Here's the reference to the documentation of the original behavior taken from http://svn.apache.org/viewvc/pdfbox/tags/1.6.0/pdfbox/src/main/java/org/apache/pdfbox/Overlay.java?view=markup