The built-in updater doesn't seem to detect the new version for me. Here's the HTTP request and response I captured via Fiddler:
GET http://www.getpaint.net/updates/versions.8.1000.0.x64.nl.txt HTTP/1.1
Host: www.getpaint.net
Connection: Keep-Alive
HTTP/1.1 200 OK
Date: Mon, 11 Jul 2016 08:09:50 GMT
Server: Apache
X-SERVER: 3683
Last-Modified: Tue, 05 Jan 2016 17:13:41 GMT
ETag: "22e-528995bee3b40"
Accept-Ranges: bytes
Content-Length: 558
Keep-Alive: timeout=5, max=100
Connection: Keep-Alive
Content-Type: text/plain
DownloadPageUrl=http://www.getpaint.net/download.html
StableVersions=4.9.5848.30436
BetaVersions=
4.9.5848.30436_Name=paint.net 4.0.9
4.9.5848.30436_NetFxVersion=4.6
4.9.5848.30436_InfoUrl=http://blog.getpaint.net/2016/01/05/paint-net-4-0-9-is-now-available/
4.9.5848.30436_ZipUrlList=http://www.getpaint.net/updates/zip/paint.net.4.0.9.install.zip,http://www.dotpdn.com/files/paint.net.4.0.9.install.zip
4.9.5848.30436_FullZipUrlList=http://www.getpaint.net/updates/zip/paint.net.4.0.9.install.zip,http://www.dotpdn.com/files/paint.net.4.0.9.install.zip