My usual browser is firefox (v2.0.0.11 as it happens). In the past I had a proxy.pac file, but now I connect direct without the need for a proxy. In firefox, I had simply clicked the "Direct connection" radio button, leaving the old value in the (now greyed-out) text field for the "Automatic proxy cofiguration URL".

The file has long since been removed, but running "javaws -viewer" gives a file not found error on stderr:

java.io.FileNotFoundException: /home/brian/config/proxy.pac (No such file or directory)
        at java.io.FileInputStream.open(Native Method)
        at java.io.FileInputStream.<init>(FileInputStream.java:106)
        at java.io.FileInputStream.<init>(FileInputStream.java:66)
        at sun.net.www.protocol.file.FileURLConnection.connect(FileURLConnection.java:70)
        at sun.net.www.protocol.file.FileURLConnection.getInputStream(FileURLConnection.java:161)
        at com.sun.deploy.net.proxy.AbstractAutoProxyHandler.getJSFileFromURL(AbstractAutoProxyHandler.java:296)
        at com.sun.deploy.net.proxy.AbstractAutoProxyHandler.init(AbstractAutoProxyHandler.java:154)
        at com.sun.deploy.net.proxy.DynamicProxyManager.reset(DynamicProxyManager.java:283)
        at com.sun.deploy.net.proxy.DeployProxySelector.reset(DeployProxySelector.java:62)
        at com.sun.javaws.Main.initializeExecutionEnvironment(Main.java:984)
        at com.sun.javaws.Main.continueInSecureThread(Main.java:170)
        at com.sun.javaws.Main$1.run(Main.java:107)
        at java.lang.Thread.run(Thread.java:619)

Truss shows that the filename seems to come from from the ~/.mozilla/firefox/.../prefs.js file, but it seems to ignore what the connection method is (direct, proxy, auto-proxy config, etc...).

It does appear to (correctly) ignore my stale entries under manual proxy configuration. No attempt is made to contact the specified proxy.

It would appear this is purely a cosmetic issue, as the operation of javaws (and any apps run from it) do not seem to be impaired.