I've done some research and I am unable to see any problem. On two separate systems I went though and deleted redundant alarms and they all deleted as they should. I also tested the "Delete After" function several times on both systems and that worked good too.
Even so, I do recall that in the past I saw a few alarms that I thought were deleted show up, so if any of the ones deleted today show up I'll have something to work with. In the mean time there are a few things you can do.
1. Change to "View Deleted" mode. Is there an unusual amount of alarms there. (There should be about 20% of the total in there at most.)
2. Change to "View All" mode. Press the "Text" column top. This will sort the database. (It also cleans it somewhat.)
3. Add a new alarm, close the window, then delete the alarm.
4. Change to "View Deleted" mode. Has the number of alarms changed?
There's a good chance going though this will solve any oddities. GigAlarm is designed to clean itself on alarm addition, but problems can happen when it adds alarms when others are active. (It can't sort the database then as the relative positions need to be constant.)
If this doesn't help please confirm that you are using the latest version
. Other than that I will need a copy of your alarm database
to investigate this further.