#!/bin/bash
s='[GUI]
Version="3.02.104"

[NOTGUI]
Version="1.05.24"

[ALSONOTGUI]
Version="3.01.230"'

sed '/^\[GUI]$/{N;s/\nVersion.*/\nVersion="3.02.108"/}' <<< "$s"
echo ""
sed '/^\[GUI]$/{n;s/Version.*/Version="3.02.108"/}' <<< "$s"