I can see problems exporting to PDF to the Windows world, but jpegs? That's pretty unusual. Again, Illustrator really shouldn't have anything to do with jpeg. You could save the file, place it in Photoshop, and save for web. As for PDF export, if you have Acrobat Distiller I'd try exporting your Illustrator files to EPS and process them in Distiller and watch the logs carefully, particularly if they involve any unusual fonts. I usually convert all fonts in Illustator to outlines first anyways if I'm exporting to a new format. Adobe export to PDF in InDesign, Illustrator, etc have had some issues in the past when I've sent spreads off to press.
It's usually best to quit out of applications after you are done with them, but OS X can stay running. I have been running continuously for 3 months without a restart. Our X server had an uptime of almost a year before a software upgrade.