G'day,
Try it with Repligo (
www.cerience.com). Seems to produce smaller files and the PPC reader program seems faster as well, to me, easier to, for want of a better word, control. It sadly doesn't work with all PDF matter but does for more modern documents. The ones I've had where it fails is a magazine converted to PDF often with line drawings (as opposed to more modern graphics) incorportaed in the text. There's a trial so see if it works for you. Despite the fact it wouldn't convert the magazine PDF's I found enough use with other file types that I bought it.
Cheers
Bern