Hi Jerry...
Try two things:
First, depending on where you get $sourceLine and $functionName from, you might have invisible newlines (especially in $sourceLine) that are making your comparisons fail. The code below is probably overkill, but try doing this and see what happens:

 
foreach $sourceLine (@SourceData) {
chomp $sourceLine; 
chomp $functionName;
if ($functionName =~ /$sourceLine/) {$counter++;}
}
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Also, use the Poor Man's Debugger, and stick print statements where you suspect your data:

 
foreach $sourceLine (@SourceData) {
print "$sourcfeLine\n"; 
print "$functionName\n"; 
print "\n"; 
if ($functionName =~ /$sourceLine/) {$counter++;}
}
[download]

And of course, use warnings; and use strict; hope that helps...
-Chris -Chris