1) The option you turned off usually prevents you from the situation 
you experience. However, since it can't know about the number of 
receivers you have at your hands, it'll keep you from channel 
switching as soon as it detects a recording (which, in its own right 
is already not easy as there is no official support for detecting 
this). I'd love to add detection for these circumstances, but right 
now, I'm unable to do so unless elgato decides to make additions to 
their AppleScript interface.

If you can give me the USB vendor and product IDs of your TV hardware 
(find them in System Profiler), I may be able to implement a smart 
workaround, though.

2) EyeTV does only respond to the Apple Remote (and thus the Virtual 
Remote) when its video window is active. Otherwise, it'll let the 
system handle it.

3) Due to one of the bugs in AppleRemote.m, which many (most? all 
except RB?) people are using to support the Apple Remote, you'll want 
to be sure to start Apple Remote supporting apps only after Remote 
Buddy has launched - as otherwise they will not detect the existance 
of the virtual AppleRemote (and/or loose control over the Apple 
Remote after a sleep/wake cycle). I don't know whether EyeTV does or 
doe snot use that sourcecode as well, though. But this just as a 
general info as it may play a role.

Best regards, 
Felix