Yep, only the last 500 reps show, because listing any more than that causes database loading delays (or somesuch technobabble).
More than once I've looked for an old thread, couldn't find it, but then I remembered someone gave me a rep point -- which, when I looked this up and clicked on the link, took me right to the thread. So reps can be a useful archive tool.
To access older (>500) rep points: I regularly save my User CP page to my hard drive as an html file (File > Save As). I usually insert the save date into the default filename so I don't overwrite any previously saved html files, e.g.
Absolute Write Water Cooler - User Control Panel 31 Mar 2008.htm
When older reps vanish from my User CP rep list I can always open a saved html file (File > Open, or just double-click on the saved html file) and find the older reps there. And if I'm online/connected and I click on an old rep link from the saved html file, it'll take me to the thread just as if I was looking at my "live" User CP rep list.
-Derek