.* is very greedy. Try this instead:

print  $#{[$lines =~ /aaa(.*?)bbb(.*?)ccc\s*dddd/gsi]} + 1 . "\n";
[download]

Update:
I went under the assumption that:

$lines = "aaa
 xxxxxxx
 bbb
    ccc
dddd";
[download]

print  $#{[$lines =~ /aaa(.*?)bbb(.*?)ccc\s*dddd/gsi]} + 1 . "\n"; will return 2.

If

$lines = "
aaa
 xxxxxxx
 bbb
    ccc
dddd
aaa
    xxxxxxxxxxxxxxxxxxxxx
    xxxxxxx
  bbb
    xxxxxxxxxxxxxxxxxxxxx
    xxxx
    xx
ccc
dddd";
[download]

print  $#{[$lines =~ /aaa(.*?)bbb(.*?)ccc\s*dddd/gsi]} + 1 . "\n"; will return 4.

If you use

$lines = "
aaa
 xxxxxxx
 bbb
    ccc
dddd
aaa
    xxxxxxxxxxxxxxxxxxxxx
    xxxxxxx
  bbb
    xxxxxxxxxxxxxxxxxxxxx
    xxxx
    xx
ccc
dddd";

print  $#{[$lines =~ /aaa.*?bbb.*?ccc\s*dddd/gsi]} + 1 . "\n";
[download]

It will return 2.
I'm not sure if thes helps or not but my guess is the last solution I show is what you want.