Looks like the problem had to do with the regex being slightly changed from the recommended Net::Telnet::Cisco prompt. The prompt should be changed from this:

Prompt => '/(?m:.*[\w.-]+\s?(?:\(config[^\)]*\))?\s?[\$#>]\s?(?:\(enab
+le\))?\s*$)/'
[download]

To this:

Prompt => '/(?m:^[\w.-]+\s?(?:\(config[^\)]*\))?\s?[\$#>]\s?(?:\(enabl
+e\))?\s*$)/'
[download]

The key difference being the ^ that marks the beginning of the line