If you pass a prefix directory to configure, and the directory exists but is not writable, the current directory is removed by configure.

This is because of this type of logic:

#process PREFIX
if [ -d "$QT_MOBILITY_PREFIX" ]; then
QT_MOBILITY_PREFIX=`absPath $QT_MOBILITY_PREFIX $LINUX_TARGET`
else
mkdir -p "$QT_MOBILITY_PREFIX"
QT_MOBILITY_PREFIX=`absPath $QT_MOBILITY_PREFIX $LINUX_TARGET`
rm -rf "$QT_MOBILITY_PREFIX"
fi
echo "QT_MOBILITY_PREFIX = $QT_MOBILITY_PREFIX" >> "$CONFIG_IN"

#process include path
if [ -z "$QT_MOBILITY_INCLUDE" ]; then
QT_MOBILITY_INCLUDE="$QT_MOBILITY_PREFIX/include"
elif [ -d "$QT_MOBILITY_INCLUDE" ]; then
QT_MOBILITY_INCLUDE=`absPath $QT_MOBILITY_INCLUDE $LINUX_TARGET`
else
mkdir -p "$QT_MOBILITY_INCLUDE"
QT_MOBILITY_INCLUDE=`absPath $QT_MOBILITY_INCLUDE $LINUX_TARGET`
rm -rf "$QT_MOBILITY_INCLUDE"
fi

The second part (around QT_MOBILITY_INCLUDE) means that it tries to create a directory in a read only location (which fails, but isn't checked). Then the absPath function attempts to change to that directory, and returns the output of 'pwd'. Since the dir doesn't exist, it returns the current directory, and then that gets removed.

The mkdir should be checked, at least.