1. $dbh is undefined, I think you need to either change $D to $dbh or vice versa.
2. $s is undefined, I think you mean $sth

Here is your stuff working and some modifications I made to show you some oddities ( that SQLite docs claim are not bugs but features...) about SQLite that I noticed right away. I don't like this rdbms because it really doesn't care what stuff you feed it. I defined an integer, but it doesn't complain when I send it something else. And you don't get an exception raised when you try to create a table with a bogus data type, which makes debuging difficult.

I would also note that attributes like NULL and NOT NULL which are required when creating tables in most all rdbms's is ignored by SQLite. Also, a DATE datatype which would benefit from right away is absent in SQLite ( you should convert all your dates to a linear value if you want to use this tool and compare inside of SQLite? )
I personally don't think I will ever use this tool. There are too many free fully featured rdbms's out there.
JamesNC

#!perl -w
use strict;
use DBI;

my $drop_tables = 1;
my $create_tables = 1;
my $dbh=DBI->connect("dbi:SQLite2:dbname=Store.db","","", {RaiseError=
+> 1}) or die "$!";
if( $drop_tables == 1 ){  #NO SUPPORT for IF EXISTS
$dbh->do("DROP TABLE ISP");
$dbh->do("DROP TABLE UnityPrimary");
$dbh->do("DROP TABLE UnitySecondary");
}
if( $create_tables == 1){
$dbh->do("CREATE TABLE ISP(Store INTEGER,Date CHAR[1] NOT NULL )") or 
+warn "$!"; #Define my own
$dbh->do("CREATE TABLE UnityPrimary(Store INTEGER,Date CHAR[9] NOT NUL
+L)");
$dbh->do("CREATE TABLE UnitySecondary(Store INTEGER ,Date CHAR[9] NOT 
+NULL )");
}
#open(CSV,"reboots.csv")||die"Can't open: $!\n";

while(<DATA>){
  chomp;
  my($store,$isp,$pri,$sec)=split /,/;
  
  my $sta=$dbh->prepare("INSERT INTO ISP(Store,Date) VALUES(?,?)");
  my $stb=$dbh->prepare("INSERT INTO UnityPrimary(Store,Date) VALUES(?
+,?)"); 
  my $stc=$dbh->prepare("INSERT INTO UnitySecondary(Store,Date) VALUES
+(?,?)");
  
  $sta->execute( $store, $isp );
  $stb->execute( $store, $pri );
  $stc->execute( $store, $sec );
}
#close CSV;

my $sth=$dbh->prepare("SELECT * FROM UnityPrimary WHERE Store > 1");
$sth->execute;

while(my@row=$sth->fetchrow_array){ print "@row\n"; }

$dbh->disconnect;

__DATA__
1,18-Oct-04,29-Oct-04,29-Oct-04
notanInt,18-Oct-04,26-Oct-04,26-Oct-04
3,21-Oct-04,26-Oct-04,11-Aug-04
4,20-Oct-04,11-Jun-04,27-Oct-04
5,18-Oct-04,3-Sep-04,24-May-04
6,17-Oct-04,15-Oct-04,15-Oct-04
[download]

OUTPUT:
notanInt 26-Oct-04
3 26-Oct-04
4 11-Jun-04
5 3-Sep-04
6 15-Oct-04
[download]