This is a problem that is driving me nuts. I have tried everything I can find to get this to resolve. When I start my computer, I get a popup that wants my icloud password. I enter it and the password is not accepted. I then go to the browser icloud log in and I can log-in just fine. iTunes has issues as well. I plug-in my iPhone 6 (IOS 8) and the program does not see the phone. I went so far as to reinstall the ios in the phone. Was better for a while but now just does not see the phone. Prior to the iphone everything worked without much trouble. But was not using iCloud sync service. I also have a pop-upo on start-up requesting my Keychain password for call.app and sometime messenger.app.
You may need to run Keychain Repair to fix a few items in it that could be problematic. This issue is apparent due to the popups from the system requesting your Keychain password.
To check keychains for problems using Keychain First Aid:
Open Keychain Access, located in the Utilites folder in the Applications folder.
Choose Keychain Access > Keychain First Aid.
Enter your user name and password.
Select Verify and click Start. ...
If there are problems, select Repair, and then click Start.
Apple KB (Note article says 10.6 but it'll work on up to 10.10)
Run the Keychain First Aid and have it repair anything that could be causing an issue. Restart the computer and see if you get the same prompts. At that point, you may need to reset the Keychain (note: this will delete all saved passwords for applications, etc):
Open Keychain Access, which is in the Utilities folder within the Applications folder.
From the Keychain Access menu, choose Preferences.
Click General, then click Reset My Default Keychain.
Authenticate with your account login password.
Quit Keychain Access.
Restart your computer.