I just noticed this happening. Very simple 7 page InDesign CS5 file. All type, 1 line art logotype placed on a master page.
When I xport as pdf, with the Adobe 'smallest file size' preset, I get a 750k pdf file. Argh. I also get a warning in the summary saying saying that 'the preset specifies that some fonts are not embedded. This application always embeds fonts.' Which I've never seen before. (I haven't edited the preset.)
I need to run pdf optimizer in Acrobat, and check all the boxes in the last two settings. This gets be down to a 65k pdf.
Any idea what's going on?
Please post in the InDesign forums.