I can't say if these problems are related to your files disappearing, but there are a couple of errors in your script:

my @files =grep { /\.jpg$/i || /\.gif/i || /\.png/i || /\.bmp/i  || /\
+.jpeg/i} readdir(DIR);
[download]

Only the first of your regexs are anchored at the end of the filename. I'd use:

my @files = grep { /\.(?:jpg|gif|png|bmp|jpeg)$/i } readdir(DIR);
[download]

Later on, you

   $file =~ m/(.[^.]+)$/;
   $ext = $1;
[download]

There's two mistakes here. The regex is wrong. You're matching any one character ("."), followed by at least one non-dot "[^.]+" at the end of the string "$". Then you assign the captured match to $ext without checking if a match was found. Don't do that.

It may be you just haven't included them in your post, but you are running under warnings and strict, aren't you?