[Android Software/Hacking General [Developers Only]] momojuro:
Hello ! I tried to fix your scripts and they work normally. I didn't find a fix for the Entropy Engine, I will do researches about it later. Just in case, test them and tell me the results ! :)

Fixed SQlite script :

#!/system/bin/sh
# "THE THING" also know as "TIM"
# (c) 2015 - By _Bon_Bon@XDA
#
# insert some useless info [HERE]
# and [HERE] ;P

TIM=/data/The_Thing/Sqlite_Vacuum&Reindex.log

# Interval between SQLite3 runs, in seconds, 172800=48 hours
RUN_EVERY=172800

if [ -e $TIM ]; then
LASTRUN=`stat -t $The_Thing | awk '{print $14}'`
else
LASTRUN=0
fi;
CURRDATE=`date +%s`
INTERVAL=$(expr $CURRDATE - $LASTRUN)

if [ $INTERVAL -gt $RUN_EVERY ];
then
if [ -e $TIM ]; then
rm $TIM;
fi;

echo "SQLite database VACUUM and REINDEX started at $( date +"%m-%d-%Y %H:%M:%S" )" | tee -a $TIM;

for i in \
`busybox find /data -iname "*.db"`;
do \
/system/xbin/sqlite3 $i 'VACUUM;';
/system/xbin/sqlite3 $i 'REINDEX;';
done;

if [ -d "/dbdata" ]; then
for i in \
`busybox find /dbdata -iname "*.db"`;
do \
/system/xbin/sqlite3 $i 'VACUUM;';
/system/xbin/sqlite3 $i 'REINDEX;';
done;
fi;

if [ -d "/datadata" ]; then
for i in \
`busybox find /datadata -iname "*.db"`;
do \
/system/xbin/sqlite3 $i 'VACUUM;';
/system/xbin/sqlite3 $i 'REINDEX;';
done;
fi;

for i in \
`busybox find /sdcard -iname "*.db"`;
do \
/system/xbin/sqlite3 $i 'VACUUM;';
/system/xbin/sqlite3 $i 'REINDEX;';
done;

echo "SQLite database VACUUM and REINDEX finished at $( date +"%m-%d-%Y %H:%M:%S" )" | tee -a $TIM;
fi;[/hide]

Fixed zipalign script :

#!/system/bin/sh
# "THE THING" also know as "TIM"
# (c) 2015 - By _Bon_Bon@XDA
#
# insert some useless info [HERE]
# and [HERE] ;P

TIM=/data/The_Thing/Zipaligner.log
ZIPALIGNDB=/data/zipalign.db

RUN_EVERY=86400

if [ -e $TIM ]; then
rm $TIM;
fi;

if [ ! -f $ZIPALIGNDB ]; then
touch $ZIPALIGNDB;
fi;

echo "Started Zipalign at $( date +"%m-%d-%Y %H:%M:%S" )" | tee -a $TIM;

#-- Zipaling /data
echo "Zipaligning /data" | tee -a $TIM;
for DIR in /data/app; do
cd $DIR;
for APK in *.apk; do
if [ $APK -ot $ZIPALIGNDB ] && [ $(grep "$DIR/$APK" $ZIPALIGNDB|wc -l) -gt 0 ]; then
echo "Already checked: $DIR/$APK" | tee -a $TIM;
else
ZIPCHECK=`/system/xbin/zipalign -c -v 4 $APK | grep FAILED | wc -l`;
if [ $ZIPCHECK == "1" ]; then
echo "Now aligning: $DIR/$APK" | tee -a $TIM;
/system/xbin/zipalign -f 4 $APK /data/local/$APK;
rc = "$?";
if [ $rc -eq 0 ]; then
if [ -e "/data/local/$APK" ]; then
cp -f -p "/data/local/$APK" "$APK" | tee -a $TIM;
rm -f "/data/local/$APK";
grep "$DIR/$APK" $ZIPALIGNDB > /dev/null || echo $DIR/$APK >> $ZIPALIGNDB;
else
echo "ZipAligning $APK Failed (no output file)" | tee -a $TIM;
fi;
else
[ -f "/data/local/$APK" ] && rm -f "/data/local/$APK"
echo "ZipAligning $APK Failed (rc: $rc)" | tee -a $TIM;
fi;
else
echo "Already aligned: $DIR/$APK" | tee -a $TIM;
grep "$DIR/$APK" $ZIPALIGNDB > /dev/null || echo $DIR/$APK >> $ZIPALIGNDB;
fi;
fi;
done;
done;

#-- Zipalign /system
echo "Zipaligning /system" | tee -a $TIM;
for DIR in /system/app; do
cd $DIR;
for APK in *.apk; do
if [ $APK -ot $ZIPALIGNDB ] && [ $(grep "$DIR/$APK" $ZIPALIGNDB|wc -l) -gt 0 ]; then
echo "Already checked: $DIR/$APK" | tee -a $TIM;
else
ZIPCHECK=`/system/xbin/zipalign -c -v 4 $APK | grep FAILED | wc -l`;
if [ $ZIPCHECK == "1" ]; then
echo "Now aligning: $DIR/$APK" | tee -a $TIM;
/system/xbin/zipalign -f 4 $APK /data/local/$APK;
rc = "$?";
if [ $rc -eq 0 ]; then
if [ -e "/data/local/$APK" ]; then
cp -f -p "/data/local/$APK" "$APK" | tee -a $TIM;
rm -f "/data/local/$APK";
grep "$DIR/$APK" $ZIPALIGNDB > /dev/null || echo $DIR/$APK >> $ZIPALIGNDB;
else
echo "ZipAligning $APK Failed (no output file)" | tee -a $TIM;
fi;
else
[ -f "/data/local/$APK" ] && rm -f "/data/local/$APK"
echo "ZipAligning $APK Failed (rc: $rc)" | tee -a $TIM;
fi;
else
echo "Already aligned: $DIR/$APK" | tee -a $TIM;
grep "$DIR/$APK" $ZIPALIGNDB > /dev/null || echo $DIR/$APK >> $ZIPALIGNDB;
fi;
fi;
done;
done;

for DIR in /system/priv-app; do
cd $DIR;
for APK in *.apk; do
if [ $APK -ot $ZIPALIGNDB ] && [ $(grep "$DIR/$APK" $ZIPALIGNDB|wc -l) -gt 0 ]; then
echo "Already checked: $DIR/$APK" | tee -a $TIM;
else
ZIPCHECK=`/system/xbin/zipalign -c -v 4 $APK | grep FAILED | wc -l`;
if [ $ZIPCHECK == "1" ]; then
echo "Now aligning: $DIR/$APK" | tee -a $TIM;
/system/xbin/zipalign -f 4 $APK /data/local/$APK;
rc = "$?";
if [ $rc -eq 0 ]; then
if [ -e "/data/local/$APK" ]; then
cp -f -p "/data/local/$APK" "$APK" | tee -a $TIM;
rm -f "/data/local/$APK";
grep "$DIR/$APK" $ZIPALIGNDB > /dev/null || echo $DIR/$APK >> $ZIPALIGNDB;
else
echo "ZipAligning $APK Failed (no output file)" | tee -a $TIM;
fi;
else
[ -f "/data/local/$APK" ] && rm -f "/data/local/$APK"
echo "ZipAligning $APK Failed (rc: $rc)" | tee -a $TIM;
fi;
else
echo "Already aligned: $DIR/$APK" | tee -a $TIM;
grep "$DIR/$APK" $ZIPALIGNDB > /dev/null || echo $DIR/$APK >> $ZIPALIGNDB;
fi;
fi;
done;
done;

touch $ZIPALIGNDB;
echo "Zipaligning finished at $( date +"%m-%d-%Y %H:%M:%S" )" | tee -a $TIM;