Updated to 5.1.5. and restore my backup, but backup was not available.

Question

I just updated to iOS 5.1.1 on my 3GS phone, previously using 5.0, while plugged into the computer and iTunes 10.6.3.  I had the phone set to backup to iCloud, and ran a sync operation before updating.  Does that not also create a backup?
When the restore process began, it asked if I wanted to set up as a new phone or restore from backup.  However the list of available backups did not have anything from today.  The last one listed was from October 2011.
So I cancelled that operation, went through the new phone setup and then it asked if I wanted to restore from iCloud.  So I chose the most recent iCloud backup which was from around 6 AM this morning.  Now it is in the process of downloading all my apps, pics, and perhaps music as well.  I don't know but it's going to take HOURS to finish this.
Anyway I opened some apps that have already downloaded, and some app data appears to be intact.  But other apps have nothing after October 2011.  And I'm talking apps that have tracked my fitness and workout progress over the past 6 months, bike rides in the past few months, car fuel fillup and maintenance history since October, I'm talking LOTS of data that appears to be gone.
What did I do wrong here?  Did I not do what I should have done regarding backups?  What is the point of backing up to iCloud if it's not going to back up all my app data???

Answer 1

Yeah this was my first time connecting my phone to the computer since I went to iOS 5.0 and iCloud, so I wasn't familiar with the fact that it did not automatically create a backup on iTunes during the Sync process.  Should have right-clicked on the phone device and did a manual backup.
But still, after restoring the backup from iCloud, I don't understand why data from certain apps got hosed (anything before October 2011, which was my last iTunes backup), while other apps' data appears to be fully intact.