I just discovered the same issue today in my efforts to get alert times synced on my iCal and iPhone after noticing a difference yesterday. I have been using the iCloud calendar sync since iCloud first came out with zero problems. Today I discover how terrible this sync is. My wife and I use a macbook, imac, 2 phones and 2 ipads to enter in calendar information and we depend on a flawless sync for our work and family schedules.
First, the iCal on my iMac has default times that get applied to every singe item, even if that item had an alert beforehand. But this default alert time is not applied as an alert on my iPhone4 calendar just the imac. I haven't even looked at my macbook yet for fear of what i may discover. After changing alerts and unchanging them and activating default times and deactivating them and wasting time doing this i just need to go through every event on my iphone to make sure that is now correct since I use that the most. What an unbelievable hassle for a program that worked flawlessly beforehand. Apple needs to recify this and have the sync work like it did before.
I am running:
Mavericks 10.9.1
iTunes 11.1.3
iCal Version 7.0 (1835.1)
iPhone4 on 7.0.4 (11B554a)