My bank (Wells Fargo) always gives me a problem, as does Smith Barney. These files have an incorrect extension. The simplest thing to do is to right-click the link in the browser and save to desktop. Then change the extension to "pdf" and open it in Preview.
I recently had an issue where, after installing Acro Reader update, the pdfs would not open in the browser (FF or Safari). even though Prview was my default application. I determined this was a bad installation of Reader.
I have Lion 10.7.3. Always in 64bit mode. And Safari 5.1.5.
I emulated your problem: I trashed all pdfviewer plugins from the InternetPlugins Folder. Emptied the Trash.
Restarted the computer. Safari would not read any pdf and downloaded them instead.
Then I reinstalled the latest version of Adobe Reader (that's how you install the pdfviewer plugin), restarted Safari and bingo: all pdf were read in Safari.
So in the meantime the Adobe pdf reader plugin works well now.