Well, I just put the hack in a stock 6.04 code, and the problem still exists. There is a problem with your cp_lib.cgi instructions with 6.04, though.
### FIND:
print FILE qq!FloodCheckSpan => q~$FloodCheckSpan~n!;
### REPLACE WITH:
print FILE qq!FloodCheckSpan => q~$FloodCheckSpan~,n!;
print FILE qq!count_views => '$in{count_views}',n!;
print FILE qq!show_topics_views => '$in{show_topics_views}'n!;
The problem is that FoodCheckSpan is not the last variable anymore. If you replace FloodCheckSpan as instructed, the new runon limit variable in 6.04 is the last one. I've found that if you replace these as instructed, the board won't run at all, because the variables are out of order. If you put your two new ones here after the new one from Infopop,
print FILE qq!runOnLimit => q~$runOnLimit~,n!;
then the board will run. However, I still have the reply problem. I find it hard to believe that this is the cause, but it's the only irregularity that I've found putting this in 6.04.
Also, the log file doesn't appear to show errors, at least I can't tell by looking at it. Due to the fact that my log is 185Mb (raw), the text editors I've tried looking at it with crash. If you could tell me what I should look try and look for, I could search for it.