Yup, I've had exactly the same problems (on server "khan"), both with download speeds and Support's seemingly apathetic response.
I too was able to (eventually) establish that it was apparently an Apache configuration issue, and that a fix had been applied to remedy the problem. Alas, this didn't seem to make the blindest bit of difference, and download speeds continued to be limited on my main domain.
If it helps, a solution that I stumbled upon was to delete web hosting for the affected domain in the control panel, and then re-apply it immediately afterwards. This appears to "re-allocate" a different version of Apache to that domain, which, if you're lucky, will circumvent any errors in the configuration of the previous version. Bear in mind that this is likely to take your site off-line for a few hours while the new dns propagates.
A good way of checking which Apache service is serving files for your domain on a particular machine is to see which ip address/hostname your domain points to; this information is also contained in the default dns records in the panel. Since I operate numerous sites, I was able to see that it was a particular ip address (and thus Apache instance) that was causing problems over a couple of domains.
One does have to wonder, however, exactly why Support were being so evasive about this issue. It took me at least 3 support tickets, countless traceroutes and loads of other bits of supporting evidence to get them to even admit there was a problem. And after all that, the "fix" hasn't made things any better. Maybe, just maybe, the claim that Dreamhost don't limit transfer speeds isn't entirely true...