Vectors output a the resolution of the device. To avoid jaggies on non-vertical or non-horizontal lines you need a lot of dots, which means very high resolution output compared to the size of the objects. They're always going to look more jagged on screen than in print, especially if you aren't zoomed in.
I never noticed strokes displaying that poorly in Acrobat, but I can replicate the same result. There is a workaround. Are you familiar with the PDF export procedure with transparency that outlines fonts? If so, turn on "Convert All Strokes to Outlines" in the Transparency Flattener Preset. This will convert a stroke to a path when exporting. If you are not familiar with method, it involves a transparent element on page, creating a Transparency Flattener Preset with this option turned on, and then exporting with Acrobat 4 compatibility.
Kool Jeffery, thanks for the workaround. I think from now on however I'll just either design vector in AI or use the rounded corners function in ID to get the same effect.