The first issue sounds like a bug in FCOM or MMM. There are a variety of issues with factions. SkyCaptain just released a small mod to try to get NPC's to stop fighting each other - it's called NPC Friendly Fire. Anyway, Oblivion XP doesn't do anything with factions. It does check for followers and if there are followers, it evaluates each one. If your follower kills something, you will get the points for it. If FCOM or MMM has assigned a follower package, the Oblivion XP might think these liches are your followers and give you points.
You can turn off some of the messages in the ini file - have a look at the Message Settings section.
1. I don't want you to repeair this. It will be dificult and usles. I just report becouse you've ordered to do it.
2. It's all in ini:
Set ObXPSettings.messageIcon to 0 ; 1
Set ObXPSettings.messageInit to 0 ; 1
Set ObXPSettings.messageSoundInit to 0 ; 1
Set ObXPSettings.messageSoundLevel to 0 ; 1
Set ObXPSettings.messageSoundXP to 0 ; 1
Set ObXPSettings.messageBufferSize to 50 ; 50
Set ObXPSettings.messageLogAutoHide to 1 ; 1