MGriffin and Strapworks-
Strapworks is correct, in that the server is looking for the index.htm page first. Then, if you do not have one, it goes from there. The reason I suggest adding one (which you would need to do via the FTP manager into your root directory) is that if it is not there, then it tries to find something else (eventually store.asp). I suspect that may be part of the cause of the 404.asp pages coming up. If it finds what the server tells it it is looking for first, I feel there may be a decrease in 404.asp page views (though I highly doubt this is even half it, just a part).
Also, the reason you are seeing these recently and not before was that recently we made an all-server-wide change to have the 404.asp page come up instead of the default page not found server page that used to come up. This does two things. The first is that it keeps your customers in the cart if they go to a bad page. Sometimes things change and a link may be bad, and you could have an advertisement that you forgot to change... This will keep your customer in the cart at least, which makes you have potential for them to keep shopping. With the old page, they would think (at least I do when I see it) that the site does not exist anymore, and just continue on. The other thing it does is that it makes your 404 hits appear on your top pages list. I believe (though am uncertain at this point) that many of these 404's occur when Google is spidering the site. Unfortunately, there is no current way to know for certain why this occurs, nor what it is looking for, but I suspect this would be the cause. These 404's were visible to you before, just in a different location where not many people checked. It was located under the Referrals > Referral Errors Menu. If you scroll back to the beginning of July, you will see all of a sudden there are 404 errors that show. There may not be as many as 404 page views, though, because the spiders can still crawl through once they hit 404.asp since there are links there for it to go through. This would not be possible with the old 404 error, so the spider would just move on.
We are still investigating all the pros and cons to this change, especially how it relates to search engines and placement. A definite con is that it raises more eyebrows since it is much more evident in Urchin that something is going on where something is not hitting your site like it thinks it should. If we find any adverse affects to this, we will change it. Conversely, if we find that there is more we can do after analyzing, we will definitely implement. Version 4.0 is going to implement other search engine optimization tactics to propel sites higher in their respective rankings, and I'm sure with the information we accumulate from then until now, we will find the most efficient and search engine friendly way to implement how a 404 error gets processed.