Index: SKMainDocument.m
===================================================================
--- SKMainDocument.m	(revision 6494)
+++ SKMainDocument.m	(working copy)
@@ -771,12 +771,20 @@
             }
         }
         if (pdfDoc) {
-            NSArray *array = [[NSFileManager defaultManager] readSkimNotesFromExtendedAttributesAtURL:absoluteURL error:&error];
-            if ([array count]) {
-                [tmpData setNoteDicts:array];
+            NSArray *array = nil;
+			// first try to read notes from .skim file
+			NSString *path = [[absoluteURL path] stringByReplacingPathExtension:@"skim"];
+			if ([[NSFileManager defaultManager] fileExistsAtPath:path]) {
+				array = [[NSFileManager defaultManager] readSkimNotesFromSkimFileAtURL:[NSURL fileURLWithPath:path] error:NULL];
+				if ([array count]) {
+					[tmpData setNoteDicts:array];
+					[self updateChangeCount:NSChangeDone];
+				}
             } else {
-                // we found no notes, see if we had an error finding notes. if EAs were not supported we ignore the error, as we may assume there won't be any notes
-                if (array == nil && isIgnorablePOSIXError(error) == NO) {
+				
+				array = [[NSFileManager defaultManager] readSkimNotesFromExtendedAttributesAtURL:absoluteURL error:&error];
+
+				if (array == nil && isIgnorablePOSIXError(error) == NO) {
                     NSAlert *alert = [NSAlert alertWithMessageText:NSLocalizedString(@"Unable to Read Notes", @"Message in alert dialog") 
                                                      defaultButton:NSLocalizedString(@"No", @"Button title")
                                                    alternateButton:NSLocalizedString(@"Yes", @"Button title")
@@ -790,32 +798,24 @@
                         [pdfDoc release];
                         pdfDoc = nil;
                     }
-                }
-                if (pdfDoc) {
-                    NSString *path = [[absoluteURL path] stringByReplacingPathExtension:@"skim"];
-                    if ([[NSFileManager defaultManager] fileExistsAtPath:path]) {
-                        NSInteger readOption = [[NSUserDefaults standardUserDefaults] integerForKey:SKReadMissingNotesFromSkimFileOptionKey];
-                        if (readOption == NSAlertOtherReturn) {
-                            NSAlert *alert = [NSAlert alertWithMessageText:NSLocalizedString(@"Found Separate Notes", @"Message in alert dialog") 
-                                                             defaultButton:NSLocalizedString(@"Yes", @"Button title")
-                                                           alternateButton:NSLocalizedString(@"No", @"Button title")
-                                                               otherButton:nil
-                                                 informativeTextWithFormat:NSLocalizedString(@"Unable to read notes for %@, but a Skim notes file with the same name was found.  Do you want Skim to read the notes from this file?", @"Informative text in alert dialog"), [[absoluteURL path] stringByAbbreviatingWithTildeInPath]];
-                            readOption = [alert runModal];
-                        }
-                        if (readOption == NSAlertDefaultReturn) {
-                            array = [[NSFileManager defaultManager] readSkimNotesFromSkimFileAtURL:[NSURL fileURLWithPath:path] error:NULL];
-                            if ([array count]) {
-                                [tmpData setNoteDicts:array];
-                                [self updateChangeCount:NSChangeDone];
-                            }
-                        }
-                    }
-                }
-            }
-        }
-    }
-    
+                } else {				
+					NSInteger readOption = [[NSUserDefaults standardUserDefaults] integerForKey:SKReadMissingNotesFromSkimFileOptionKey];
+					if ([array count] && readOption == NSAlertOtherReturn) {
+						NSAlert *alert = [NSAlert alertWithMessageText:NSLocalizedString(@"Found Embedded Notes", @"Message in alert dialog") 
+													 defaultButton:NSLocalizedString(@"Yes", @"Button title")
+												   alternateButton:NSLocalizedString(@"No", @"Button title")
+													   otherButton:nil
+										 informativeTextWithFormat:NSLocalizedString(@"Unable to read .skim file for %@, but Skim notes were found in the Extended Attributed.  Do you want Skim to read these?", @"Informative text in alert dialog"), [[absoluteURL path] stringByAbbreviatingWithTildeInPath]];
+						readOption = [alert runModal];
+					}
+					if (readOption == NSAlertDefaultReturn) {
+						[tmpData setNoteDicts:array];						
+					}
+				}
+			}
+		}
+	}
+		
     if (data) {
         if (pdfDoc) {
             didRead = YES;