There are 2 most common reasons that you may obtain an output PDF that is bigger than the original PDF after optimization.
In a PDF document, the reference table – which is the table that indicates where each objects is located in the file – can be compressed as what is known as a cross reference stream. See PDF Specifications “3.4.7 Cross-Reference Streams”.
Update: This issue is resolved as of v2017R1. We’ve added an option to re-compress the reference table and object streams. Make sure to use the optimization settings below to resolve this issue:
For this type of documents, Qoppa’s optimizing library jPDFOptimizer is able to read the reference table appropriately but is not, at the moment, able to re-compress the object stream upon saving the document. And so it is possible that the output ‘compressed’ PDF is a bit larger than the original original (if it also happens that other compression functions were negligible in size).
We’re planning to support re-compressing the reference table soon. If you are running into this issue, email us so we can keep track of how often this issue occurs and prioritize this fix accordingly.
Sometime when recompressing images, you may obtain bigger images in the output PDF than in the original file. You will need to look at the compression and quality used. If you are using JPEG2000 or JPEG compression, you can try using a lower quality settings.