Have you output your file to Acrobat 5 or higher? Check your settings. Go to File menu/PDF export presets and pick Press. Make sure the Compatablity setting is to 5 - supporting alpha channels and transparency. Acrobat 4 has problems with these.
If you're using Distiller, open it and go to the Settings menu and make a setting that copies Press but is compatable with Ac 5. If printing a postscript file for distilling, select All under Graphics/images/Send Data. Under Advanced, select High Resolution under Transparency Flattener.
You might also try checking your transparency flattening Presets in ID - under Edit menu - set to High resolution.
Try printing it out of ID to see if you get problems. If so, you did something in ID.
After you make your pdf open it and go to the Advanced menu. Select Overprint preview and look at the pdf for problems. Then go to Transparency Flattener preview and see if anything's amiss