Windows 7 - certain sites work in proxy, but not in my browsers

I have a recent problem with trying to browse a couple of my regular websites. When I try to view them I get "Firefox can't establish a connection to the server at" messages, instantly with no even trying to access the domains. I tried ping and tracert commands in the command prompt, and both failed to connect to the domains. However, when I go to any proxy/unblocking website and enter these sites, they will load fine through proxy so I know they're online. They were showing up as "down for everyone" a few days ago, checking via websites that check domains, but they're working now.

I checked my hosts file, they're not being blocked through that. It's not a Firefox issue as even IE won't load them. I said before, they'll load via proxy websites but not in my browsers through normal use. I have no idea what's blocking these sites or why I can't view them. Could it be an issue on the server's end not letting me connect? Blocking via my ISP? Or just some other thing with my PC? Though I can't think of why these 2 specific sites would be giving me problems, neither is related to antivirus or whatever and all my scans with MSE and Malewarebytes are coming up clean for malware. I did run Windows Update a few days ago, but it was mostly MSE definition updates and 1 Windows 7 update, nothing really special, and I think this started well after I ran the update. As it is I'm basically clueless. And even though I can load them in proxy sites I can't use them as they don't really work through free proxies due to javascript and such.

Hi Diosoth,

You may try if possible for you to connect to a Free Wi-Fi Hotspots just to see if it has nothing to do with your ISP. Some DNS's may be changed or update by your ISP. Your ISP doesn't normally inform their clients of these changes, I have experienced this myself.

Other than using Proxy's, Public DNS's might also help.

I would guess it's a problem with ISP dns.
when you say "I tried ping and tracert commands in the command prompt, and both failed to connect to the domains." did you ping IP address or domain name like google.com
to be sure resolve sites IP you can do it by pinging from proxy where site is ok. in the response you should see sites IP address (number like 173.194.65.103 or something like that)
try to enter that number in your browser address bar, can you connect?

Nothing I've tried has worked, and the problem seems to be getting worse. I keep finding more sites that will not load in my browser, but will load if I go to a proxy website and enter the URL. It's further annoying because some of the download servers used by nexusmods.com are affected. I can't rely on these proxy sites for browsing because they often do not fully support javascript or other site features/code.

The only malware programs I actively run are Microsoft Security Essentials and Malwarebytes. Could either of them be causing problems? I've tried clearing cache and cookies but this is also affecting sites I have never been to.

I just tried "ipconfig /flushdns" and got no results. I also switched over to Google's Public DNS, linked above, and I still could not access these same sites. On top of that, restarting my modem took a while and I didn't think it was going to connect, and my web browsing was a bit slower, so I switched back to the defaults. Clearing cache and site cookies didn't do anything, nor does it explain why I have this issue with sites I've not been to before.