thanks for asking.

It shouldn't matter too much which entry is first in the Login Items 
pane. Remember OS X is a multitasking operation system and it seems 
to launch all of the Login Items at once (or shortly after each 
another). I've had Safari and Mail in my Login Items a while back and 
they were both bouncing around happily in the Dock.

What is happening on your Macs is probably this:

1) EyeTV and Remote Buddy start up - at once.

2) EyeTV is quicker with grabbing the Apple Remote.

3) Remote Buddy tries a technique to make EyeTV drop control over the 
remote, but it fails for timing reasons, as EyeTV can probably not 
respond in a timely fashion while the system is still occupied with 
startup tasks that eat plenty of CPU and I/O resources. The technique 
works fine, if there is less load on the system - but it can fail in 
this situation of high load. That's why it'll work sometimes - and 
not work at other times you start up your Mac.

The (definitive) solution for this problem will hopefully finally 
make it in the next release of Remote Buddy.

Best regards, 
Felix