Sorry about the late response.
Do you use any antivirus? What about extensions?
I dont have any antivirus running in the background, but I do have MalwareBytes scanner installed. As for extensions, the problem still happens when there are none enabled.
Do you have a couple of example links of those problematic downloads?
This is the only one that I know of, but I've seen it happen on other ones too: http://youtube-dl.org/downloads/latest/youtube-dl.exe
This is the message I get on my Downloads tab: http://imgur.com/EkgVDAm (Translation: Stopped: Virus Detected)
Also, I dont think anything else is blocking the file on my computer, since I'm able to download it just fine using firefox.