I've got a similar problem but the other way round.
My PDF file exported from InDesign CS5 is bigger than from CS6.
Same settings, high quality export without downsampling, compression: automatic (JPEG).
My only guess is, that something has changed with the jpeg compression...?
It's acutally no problem, if I can go sure, that there's no loss in quality with CS6 Export.
Has anyone an explanation?
Quite a bit of work has been done for InDesign 8 (CS6) to further optimize the generated PDF compared with earlier versions of InDesign, especially if you have graphics on master pages.
Unless we have the actual sample files to look at, we can't speculate as to the anomalies you see. It isn't our experience and we don't know what could be causing what you are seeing as files 350% larger than previously generated. No, we didn't have any JPEG compression change that would account for this assuming you used the exact same JPEG (Automatic) settings.
Thanks for your answer.
So I don't have to fear any loss in quality compared with CS5-exported PDF?
I was just confused about the file size ...
There is no loss of quality assuming you use the same settings. What was trimmed was unnecessary metadata as well as unnecessarily-repeated graphics definitions within the PDF file.