While the error message(s) seems FAIRLY obvious... it is perhaps misleading. The fact that your .html page loads despite inoperable links is not terribly relevant. But the inoperable links are!

To my eyes, your problem is trying to execute a script from an <a href...

Customarily, one would use a form whose action = the file you wish to execute. Since it you're running on a windows server (1. sorry, no knowledge there; 2. It would be helpful to tell us, explicitly, rather than require us to draw inferences from your error!!), you may be able to make the .bat file the action, directly, but if not fall back on your (misleadingly named) "runindex.pl" in a valid .html form.

You may wish to note that TTBOMK, ISPs and sysadmin rarely use the directory containing publicly available .html as a directory in which a (update specifying perl, in light of .php, etc) perl script is executeable. That may also have something to do with your error... Customarily, scripts go into a cgi-bin directory (location determined by the sysadmin or ISP)

...and, overall, the bits of information and code you've provided are not -- at least for me -- adquate to diagnose your problem. Please, Update with additional code, system info, etc.