I get a message that there is an updated verson of Remote Buddy available, would I like to download it? I say, "yes".

Stuff happens. It asks me to reboot Remote Buddy. Yes.

More stuff happens, then, Remote Buddy completely vanishes. It's not on my hard drive anymore. Quicksilver can't find it. Spotlight can't find it. I have to go to the website to download and install it again. Then everything is fine.

Mac mini, Intel Core Duo, OS 10.4.9 

I have a similar problem. 
When RB tells me, there is a new version available, it downloads it, does some stuff, finishes and tells me, my version is updated. 
But it is not. 
I have to manually download and install, then it is fine.

Did you install Remote Buddy in /Applications or elsewhere?

Do you run as admin user or user with limited rights on your machine?

What happens during an update of Remote Buddy itself is this:

1) Remote Buddy downloads the latest DMG file (the one you get from 
the website).

2) Then launches a special tool inside Remote Buddy, that mounts the 
DMG in the background and replaces the old copy with the new one.

3) Launch the new version of Remote Buddy.

Since it will only offer you to proceed after step 1 if the download 
completed successfully, the problem is probably located in step 2. As 
Remote Buddy uses standard system tools to achieve what it does 
there, the only two remaining error sources I can see are

a) permissions to write to the directory Remote Buddy is located in 
are to restrictive

b) inavailability of the shell commands Remote Buddy uses (corruption 
of those can easily happen while running (any) software while Apple's 
Software Update is running - my source for this is http:// 
unsanity.org/archives/mac_os_x/shock_and_awe.php ).

There may be more possible error sources, but these spring to mind at 
first.

Best regards, 
Felix 

I typically run in a non-administrative account, authorizing activity with an admin log-in when necessary. If I'm remembering correctly, the installer does ask for my authorization (and then I give it).

Next time I'll try repairing permission first. 

I'll spend more time on this part of the updater to handle this edge 
case, too, as time permits.

Best regards, 
Felix 

Might also point out that after I manually reinstall Remote Buddy it defaults to displaying in the dock despite the setting in RB preferences. Toggling dock display on and off solves this.

e. 

The latter is normal, though. Whether Remote Buddy appears in the 
dock or not is controlled by the NSUIElement property in its 
Info.plist file. Updating through Online Update will add or remove 
this entry according to the previous state of Info.plist, but we run 
into a classic hen-egg-problem with manual updates - Remote Buddy 
would need to run to update its own Info.plist. However, the 
NSUIElement entry is already there at launchtime and can't be changed 
at runtime.

Best regards, 
Felix