How to stop iCal from automatically adding alarms to new events

iOS 5 and iCloud should be coming out tomorrow. There should be improvements in this area. Hopefully this will help you. I know it is not what you would want to hear, but I have seen disappearing content like you describe. Especially with Exchange, and OS 10.6.x

To set single alerts on all birthdays, you can avoid a script altogether:

1. Open Calendar Preferences in Calendar.
2. Under General, tick "Show Birthdays calendar".
3. Under Alerts, set an alert for "Birthdays".

I haven't taken the time to actually write up an AppleScript for the double alarm parts, but this article seems to cover scripting calendar alarms quite nicely. I would imagine you would just need to create a file or list in the script that contains the names of the events (which you can deduce from the standard naming convention Calendar app uses).

Also I am using Mountain Lion with Calendar app. I can't recall if the steps above work on older versions of iCal.