I cannot reproduce your results on ActivePerl for Windows. Are you sure each "orgtext" is on a different line? $. is the current input line number, not the number of substitutions performed.

	a.html	b.html
Before	orgtext orgtext orgtext orgtext [download]	orgtext orgtext orgtext orgtext [download]
After	1 1 2 3 [download]	4 4 5 6 [download]

Perhaps you want

perl -pi -e 's/orgtext/++$x/eg;' *.html
[download]

	a.html	b.html
After	1 2 3 4 [download]	5 6 7 8 [download]

or

perl -pi -e 's/orgtext/++$x/eg; $x=0 if eof(ARGV)' *.html
[download]

	a.html	b.html
After	1 2 3 4 [download]	1 2 3 4 [download]

Update: Compacted node by replacing lists with tables.

Hmm. I am running perl, v5.8.8 built for i486-linux-gnu-thread-multi.

The result I want is:



	a.html	b.html
Before	orgtext orgtext orgtext orgtext	orgtext orgtext orgtext orgtext
After	1 2 3 4	1 2 3 4



But the result I get is:



	a.html	b.html
After	1 1 2 3	1 1 2 3

I've already explained why your code produces the a.html you're seeing.

Your code should not produce the b.html you are seeing unless you are wrong about your input, you are wrong about your code, you are wrong about your output, or your Perl is broken.

I've already shown the code that will get you what you want, so what you are asking now?