I have noticed when backing up the database through the control panel if you do not delete all the files in the backup folder it will not over write these files leaving you with an incomplete backup of your site.

Has anyone else noticed this?

I am not really sure. I never really checked
How did you catch this?(Date stamp?)

It appears to be working okay for me.
File sizes and date stamp changed. But I did select the drop table option.

Well, a long story short.

We suffered a severe crash and I had to restore the database from my most recent backup . When I tried to restore it I was missing quite a few members and about 50,000 post's.

I retrieved the actual files from the mysql database on the dead hard drive to recover the site.

Humm. I have never had to recover ubb from a crash but I have moved twice. But to be honest when I moved I did not use the UBB flavor backup.
I switch back and forth with backups,UBB,PHPmyadmin,Cpanel,ETC
So again I am not sure if the ubb method has a flaw.

I used the raw mysql files directly off the hdd. uploaded them into the proper folder, changed to owner and group of mysql, chmod them properly and then do the proper chmod on the folder.

I seriously doubt that anyone here will ever do it that way as it requires root and super user server access.

As a thought I would probably never use the ubb backup to restore. Unless it was a last ditch effort. Since it would be a import 65 times. Unless someone will chime in and tell me different because I don't see any way to import 65 files all at once.

I've done that, it definitely requires that you know what you're doing though lol...

And if you don't your gunna get a crash course, LOL.

I have the entire process backed up into single backup files for MySQL, PHP, and DB every day so most I can lose is about a day of posts which we're okay with. I could implement continuous but that would put a bit more of a hit on the drives that for our purpose isn't really needed.

Any features gets broken and I can easily replace it quickly, but I do have root/admin access and Remote Desktop access on Windows Server 2003.

Yeah, I don't use windows. It's a bit more difficult without a point and click operating system for those who don't know what they are doing.