What makes you think the variables aren't being passed in to your function?

You have several problems. One of the most serious is that you're parsing (what looks like) XML with regular expressions and you aren't checking to see if the regexes match. Another problem is that you're using global variables. Why are you bothering to return variables from your functions if you're not going to use them? (By the way, your returns are still broken. Why should I give you further advice if you ignored my previous advice? I don't know.)

The problem you're seeing right here is that you're trying to call check_gene_seq() with variables that may or may not be defined, and that may or may not come from the line you're currently processing. Another comment recommend using lexicals and a hash, and I agree. You'll probably get a much better payoff if you use a real XML parsing module though.