This posting is older than 6 months and can contain outdated information.
The fix should be quite easy:
go to ~/Library/Preferences/ and look for a file named something like
com.iospirit.remotebuddy.com.apple.remote.com.elgato.eyetv. 
5cc7e4000000ee.plist
(the 5cc7e4000000ee may differ, but should be equally long)
The com.elgato.eyetv.5cc7e4000000ee part means this:
com.elgato.eyetv - the raw receiver 
5cc7e4000000ee - the raw ID of the remote
The problem is that the raw ID in this case actually is just "ee" and 
there was a bug in V1.8 where a 32 bit integer would be used like a 64 
bit one, thus the first four bytes are more or less random. That 
longer - and pretty random rest (different on each start for some) - 
shouldn't have been there in the first place and was fixed in V1.8.1.
Solution:
Set any button on the "empty" / reset mapping tables and quit Remote 
Buddy. A new file is now generated, from which you can get the correct 
filename, in this case that'd be
com.iospirit.remotebuddy.com.apple.remote.com.elgato.eyetv.ee.plist
With Remote Buddy quit (important), first make a backup copy of your 
old prefs file, then rename the old file to the correct - and stable - 
name. In this case, that would mean to rename
com.iospirit.remotebuddy.com.apple.remote.com.elgato.eyetv. 
5cc7e4000000ee.plist
to
com.iospirit.remotebuddy.com.apple.remote.com.elgato.eyetv.ee.plist
That you're offered less buttons with a reset mapping table is simple 
to explain: the reset mapping table has almost all buttons pre- 
occupied in the global mappings table to send the button press back to 
EyeTV.
Hope that  helps.
Best regards, 
Felix