comments popup window erros

I loaded up wordpress a few days ago onto my university account & have been having some odd problems. My site is at http://www.oregonstate.edu/~vanbossd/
When someone clicks on the comments link at the bottom of each post, the popup window comes up and has 4 or 5x the content it should. in other words, theres 4 or 5 places to enter name, email, website, comment, and hit submit. comments still seem to work in some tests i’ve done, but still it doesn’t look so hot.
Also, i’ve been having problems with extra slashes being thrown into links generated by the code. For instance, http://oregonstate.edu/~vanbossd//index.php/m/200309#post-10
there should only be one slash before the index.php. luckily my server is forgiving and allows most of that stuff by. However, i think that might be causing some of the problems ive been seeing when i click on the category name or the name of the post. that link that i posted brings up a site without any of my css formatting. i’m not very well versed with PHP so it could be something very obvious i’m missing…
I was wondering if maybe my DHTML menus could be causing the problem? since i installed wordpress, periodically the links give extra slashes. it seems to only happen when i get one of those strange unformatted pages to come up and try to use the dhtml menu.
a friend who also runs wordpress on the same servers has had almost no problems but he used one of the canned index.php’s.
anyone have some insite?
oh one other thing, i’m using the latest beta which took care of one of my earlier problems with being able to install at all.