I've noticed that after editing code in an HTML box, the selected object is sometimes something other than the HTML box. Thus, using Ctrl + c to copy the HTML after editing it actually copies a different object.

It seems to happen slightly randomly, however. Is this a known VSD bug?

Do you have an example? I'm not sure what you're describing here (maybe I'm just dense). I've used html boxes on all my sites with no problems.
Are you saying that you've copy/pasted the actual html box to another page or location and something else got copied instead?

The problem I'm having is that sometimes while working with the program, the last selected object isn't always the currently selected object.

Here's what happened: I edited the html in an html box, clicked ok, used CTRL + c, used CTRL + v on a different page. The pasted object was not the html box I just finished editing, it was another one on the first page.

This isn't a copy/paste issue, as when I looked back on the first page the selected object was the one pasted, but rather the fact that I never selected that object is highly displeasing! These steps don't always produce the error, and seem to only happen once per session.

I tried to duplicate your issue but couldn't get it to rear its ugly head.

Not that big a deal, just wondering if anyone's seen it before.