I seem to be having the same issue as an earlier poster. Default homepage saves but the rest of the preferences don't. I have quadruple checked all the actions and outlets and ib relationships. I have removed all ignorecontent code but atlas can't get autoload images to save or javascript. if I reverse the yes and the NO here then atleast images load.:

if ([autoloadImages state] == NSOffState){
[p setLoadsImagesAutomatically:NO];
}
else {
[p setLoadsImagesAutomatically:YES];
}

any help would be greatly appreciated
here is all the code for controller.m:

#import "Controller.h"
#import <WebKit/WebPreferences.h>

@implementation Controller

- (void)awakeFromNib
{
md = [MyDocument alloc];
[md init];

WebView *wv = [WebView alloc];
[wv init];
[wv setPreferencesIdentifier:@"PREF"];

p = [wv preferences];
[p setAutosaves:YES];

NSUserDefaults *defaults;
defaults = [NSUserDefaults standardUserDefaults];
NSString * dHomepage = [defaults stringForKey:@"defaultHomepage"];
if (dHomepage != nil) {
[md setDefaultHomepage:dHomepage];

}

}

- (IBAction)apply:(id)sender
{
NSUserDefaults *defaults;
defaults = [NSUserDefaults standardUserDefaults];

NSString* dHomepage = [defaultHomepage stringValue];
[defaults setObject:dHomepage forKey:@"defaultHomepage"];
[md setDefaultHomepage:dHomepage];

[p setAutosaves:YES];

if ([autoloadImages state] == NSOffState){
[p setLoadsImagesAutomatically:NO];
}
else {
[p setLoadsImagesAutomatically:YES];
}

if ([allowAnimatedImages state] == NSOffState){
[p setAllowsAnimatedImageLooping:NO];
}
else {
[p setAllowsAnimatedImageLooping:YES];
}

if ([javascriptEnabled state] == NSOffState){
[p setJavaScriptEnabled:NO];
}
else {
[p setJavaScriptEnabled:YES];
}
}

- (void)windowDidBecomeKey:(NSNotification *)aNotification
{
[defaultHomepage setStringValue:[md getDefaultHomepage]];

[p setAutosaves:YES];

if ([p loadsImagesAutomatically]){
[autoloadImages setState:NSOnState];
}
else {
[autoloadImages setState:NSOffState];
}

if ([p allowsAnimatedImageLooping]){
[allowAnimatedImages setState:NSOnState];
}
else {
[allowAnimatedImages setState:NSOffState];
}

if ([p isJavaScriptEnabled]){
[javascriptEnabled setState:NSOnState];
}
else {
[javascriptEnabled setState:NSOffState];
}
}

@end

here is the code for controller.h:

/* Controller */

#import <Cocoa/Cocoa.h>
#import <WebKit/WebPreferences.h>
#import <WebKit/WebView.h>

#import "MyDocument.h"

@interface Controller : NSObject
{
IBOutlet id allowAnimatedImages;
IBOutlet id autoloadImages;
IBOutlet id defaultHomepage;
IBOutlet id javascriptEnabled;

WebPreferences *p;
MyDocument *md;
}
- (IBAction)apply:(id)sender;

@end