Well I think you got me going on a good track of checking different HTTP headers and re-examining the example at http://empireenterprises.com/_comet.html
Unfortunately I still have no luck with IE with different headers, meta tags, regular tags, etc. I re-examined the example and saw that he's not printing javascript functions at all, but rather just JSON objects. JSON is useless unless it is evaluated, so I think that he is somehow actually accessing the innerHTML during page load in IE (unfortunately have not been able to contact him). His client code obviously does this but I have no idea how the server gets IE to work (I even tried the exact same headers and tags).
I tried a new test to see if the script may be executing but not interacting by setting a variable to the current Javascript time in each step, waiting two seconds, then setting again. The last time I used an alert() to print the values. Firefox - three different times, IE - same time.
The other major working example is here:
http://meteorserver.org/
The code is much more complicated, but they also created a Perl server. I am not able to pick it apart enough to tell what is wrong with mine. Ugh - I thought for sure something would give me hope today.