Eu não tenho esse problema de alternar entre um documento do emacs, uma cauda de /var/log/system.log e uma janela superior na tela.
Eu exportei as configurações atuais do meu terminal e elas são as seguintes:
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE plist PUBLIC "-//Apple//DTD PLIST 1.0//EN" "http://www.apple.com/DTDs/PropertyList-1.0.dtd">
<plist version="1.0">
<dict>
<key>BackgroundAlphaInactive</key>
<real>0.74631954479768781</real>
<key>BackgroundBlur</key>
<real>0.0</real>
<key>BackgroundBlurInactive</key>
<real>0.0</real>
<key>BackgroundColor</key>
<data>
YnBsaXN0MDDUAQIDBAUGFRZYJHZlcnNpb25YJG9iamVjdHNZJGFyY2hpdmVyVCR0b3AS
AAGGoKMHCA9VJG51bGzTCQoLDA0OV05TV2hpdGVcTlNDb2xvclNwYWNlViRjbGFzc0cw
IDAuOTgAEAOAAtIQERITWiRjbGFzc25hbWVYJGNsYXNzZXNXTlNDb2xvcqISFFhOU09i
amVjdF8QD05TS2V5ZWRBcmNoaXZlctEXGFRyb290gAEIERojLTI3O0FIUF1kbG5wdYCJ
kZSdr7K3AAAAAAAAAQEAAAAAAAAAGQAAAAAAAAAAAAAAAAAAALk=
</data>
<key>BackgroundSettingsForInactiveWindows</key>
<true/>
<key>CursorBlink</key>
<true/>
<key>CursorColor</key>
<data>
YnBsaXN0MDDUAQIDBAUGFRZYJHZlcnNpb25YJG9iamVjdHNZJGFyY2hpdmVyVCR0b3AS
AAGGoKMHCA9VJG51bGzTCQoLDA0OV05TV2hpdGVcTlNDb2xvclNwYWNlViRjbGFzc0sw
LjMwMjQxOTM2ABADgALSEBESE1okY2xhc3NuYW1lWCRjbGFzc2VzV05TQ29sb3KiEhRY
TlNPYmplY3RfEA9OU0tleWVkQXJjaGl2ZXLRFxhUcm9vdIABCBEaIy0yNztBSFBdZHBy
dHmEjZWYobO2uwAAAAAAAAEBAAAAAAAAABkAAAAAAAAAAAAAAAAAAAC9
</data>
<key>Font</key>
<data>
YnBsaXN0MDDUAQIDBAUGGBlYJHZlcnNpb25YJG9iamVjdHNZJGFyY2hpdmVyVCR0b3AS
AAGGoKQHCBESVSRudWxs1AkKCwwNDg8QVk5TU2l6ZVhOU2ZGbGFnc1ZOU05hbWVWJGNs
YXNzI0AsAAAAAAAAEBCAAoADVk1vbmFjb9ITFBUWWiRjbGFzc25hbWVYJGNsYXNzZXNW
TlNGb250ohUXWE5TT2JqZWN0XxAPTlNLZXllZEFyY2hpdmVy0RobVHJvb3SAAQgRGiMt
Mjc8QktSW2JpcnR2eH+Ej5ifoqu9wMUAAAAAAAABAQAAAAAAAAAcAAAAAAAAAAAAAAAA
AAAAxw==
</data>
<key>FontAntialias</key>
<true/>
<key>FontWidthSpacing</key>
<real>0.99596774193548387</real>
<key>Linewrap</key>
<true/>
<key>ProfileCurrentVersion</key>
<real>2.02</real>
<key>SelectionColor</key>
<data>
YnBsaXN0MDDUAQIDBAUGFRZYJHZlcnNpb25YJG9iamVjdHNZJGFyY2hpdmVyVCR0b3AS
AAGGoKMHCA9VJG51bGzTCQoLDA0OVU5TUkdCXE5TQ29sb3JTcGFjZVYkY2xhc3NGMCAw
IDEAEAKAAtIQERITWiRjbGFzc25hbWVYJGNsYXNzZXNXTlNDb2xvcqISFFhOU09iamVj
dF8QD05TS2V5ZWRBcmNoaXZlctEXGFRyb290gAEIERojLTI3O0FITltiaWttcn2GjpGa
rK+0AAAAAAAAAQEAAAAAAAAAGQAAAAAAAAAAAAAAAAAAALY=
</data>
<key>ShowShellCommandInTitle</key>
<true/>
<key>ShowWindowSettingsNameInTitle</key>
<false/>
<key>TerminalType</key>
<string>vt102</string>
<key>TextBoldColor</key>
<data>
YnBsaXN0MDDUAQIDBAUGFRZYJHZlcnNpb25YJG9iamVjdHNZJGFyY2hpdmVyVCR0b3AS
AAGGoKMHCA9VJG51bGzTCQoLDA0OVU5TUkdCXE5TQ29sb3JTcGFjZVYkY2xhc3NPEB0w
Ljk4MTE0OTkwNDUgMSAwLjA0ODk0MDY0OTEyABABgALSEBESE1okY2xhc3NuYW1lWCRj
bGFzc2VzV05TQ29sb3KiEhRYTlNPYmplY3RfEA9OU0tleWVkQXJjaGl2ZXLRFxhUcm9v
dIABCBEaIy0yNztBSE5bYoKEhouWn6eqs8XIzQAAAAAAAAEBAAAAAAAAABkAAAAAAAAA
AAAAAAAAAADP
</data>
<key>TextColor</key>
<data>
YnBsaXN0MDDUAQIDBAUGFRZYJHZlcnNpb25YJG9iamVjdHNZJGFyY2hpdmVyVCR0b3AS
AAGGoKMHCA9VJG51bGzTCQoLDA0OVU5TUkdCXE5TQ29sb3JTcGFjZVYkY2xhc3NPECgw
LjgyNDA5NTkzMjkgMC44Mzk5Mjg2Njg1IDAuMDQxMTA2NjU0MjUAEAGAAtIQERITWiRj
bGFzc25hbWVYJGNsYXNzZXNXTlNDb2xvcqISFFhOU09iamVjdF8QD05TS2V5ZWRBcmNo
aXZlctEXGFRyb290gAEIERojLTI3O0FITltijY+RlqGqsrW+0NPYAAAAAAAAAQEAAAAA
AAAAGQAAAAAAAAAAAAAAAAAAANo=
</data>
<key>name</key>
<string>Pro</string>
<key>shellExitAction</key>
<integer>1</integer>
<key>type</key>
<string>Window Settings</string>
<key>warnOnShellCloseAction</key>
<integer>0</integer>
</dict>
</plist>
Espero que você não tenha usado a barra de rolagem nas outras telas ...
Uma coisa que você pode tentar é configurar sua variável $ TERM para vt102; O meu foi definido para 'screen'. Se você me informar se há um modo específico que você está usando, ou um tipo de arquivo que eu poderia editar para duplicar o problema, vou procurar mais por você ...