I use an http proxy set up like this:
Tools/Options/Proxy Settings/[More]
[x] Proxy Requires Authentication
Username: ...
Password: **********

Whether I check "Tools/Servers/Java/Use IDE's proxy setting" checkbox or not, autoupdate keeps popping up the empty proxy auth dialog.

FINE [glassfish]: HTTP Command: http://localhost:4848/__asadmin/version
INFO [org.netbeans.core.NbProxySelector]: Incomplete SOCKS Server [/] found in ProxySelector[Type: 2] for uri socket://localhost:4848. 
FINER [glassfish]: AdminAuthenticator.getPasswordAuthentication() with prompt Squid proxy-caching web server
WARNING [glassfish]: No authentication set while requesting http://updates.netbeans.org/netbeans/updates/7.1.2/uc/final/certified/catalog.xml.gz?unique=NB_GFMOD_JAVA_WEBEE034f09f66-54c4-4129-9bc8-cea0913e392a_403a1058-6e73-4ab4-9bb7-ccfa81ede2e0
INFO [org.netbeans.modules.autoupdate.updateprovider.DownloadListener]: Reading URL http://updates.netbeans.org/netbeans/updates/7.1.2/uc/final/certified/catalog.xml.gz?unique=NB_GFMOD_JAVA_WEBEE034f09f66-54c4-4129-9bc8-cea0913e392a_403a1058-6e73-4ab4-9bb7-ccfa81ede2e0 failed (java.io.IOException: Server returned HTTP response code: 407 for URL: http://updates.netbeans.org/netbeans/updates/7.1.2/uc/final/certified/catalog.xml.gz?unique=NB_GFMOD_JAVA_WEBEE034f09f66-54c4-4129-9bc8-cea0913e392a_403a1058-6e73-4ab4-9bb7-ccfa81ede2e0)
INFO [org.netbeans.modules.autoupdate.ui.Utilities]: Server returned HTTP response code: 407 for URL: http://updates.netbeans.org/netbeans/updates/7.1.2/uc/final/certified/catalog.xml.gz?unique=NB_GFMOD_JAVA_WEBEE034f09f66-54c4-4129-9bc8-cea0913e392a_403a1058-6e73-4ab4-9bb7-ccfa81ede2e0
java.io.IOException: Server returned HTTP response code: 407 for URL: http://updates.netbeans.org/netbeans/updates/7.1.2/uc/final/certified/catalog.xml.gz?unique=NB_GFMOD_JAVA_WEBEE034f09f66-54c4-4129-9bc8-cea0913e392a_403a1058-6e73-4ab4-9bb7-ccfa81ede2e0
	at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1615)
	at org.netbeans.modules.autoupdate.updateprovider.NetworkAccess$Task$2.call(NetworkAccess.java:146)
	at org.netbeans.modules.autoupdate.updateprovider.NetworkAccess$Task$2.call(NetworkAccess.java:136)
	at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334)
	at java.util.concurrent.FutureTask.run(FutureTask.java:166)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1110)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:603)
	at java.lang.Thread.run(Thread.java:722)

Based on the source, I found a workaround: I have to add the lines
"useProxyAuthentication=true
proxyAuthenticationUsername=myusername
proxyAuthenticationPassword=cleartextpassword"
to config\Preferences\org\netbeans\modules\glassfish\common.properties.

I don't get the point of org.netbeans.modules.glassfish.common.ProxySettings. Why not use the core ProxySettings or its settings?