What might be a problem, is that the /i modifier is not working the way you might expect. I think you don't want to mind about the capitalisation of your tags, ie. %TAG%, %tag% and %tAg% should all be equivalent.

If this is the case, you have to store all your templates lowercase (or upper, doesn't make a difference) and then convert the captured string ($1) to this case. The /i modifier has only an influence on how the matching is done, the captured string is always exactly as it was in the original:

'Hello World' =~ /(hello)/i;
print $1; # prints 'Hello'
[download]

So to solve your problem, you can take advantage of the /e modifier and write something like this:

my %template = (
        tag1    => 'test1',
        tag2    => 'test2',
);

while (<DATA>) {
  print "before: $_";
  s/%([^%]+)%/$template{lc($1)}/ge;
  print "after:  $_";
}

__DATA__
%tag1% some text %TAG2% some more text
[download]

-- Hofmator