why would the fork() interfere with the results from the backticks in line 8?
It could, if you'd have your own SIG{CHLD} handler, but you don't.
In second your example you are performing 1 fork call per @dir entry, and in first for each @dir entry * each @makelist entry
So those two examples are completelly different
I would suggest to minimize it to proof-of-concept code, so everyone could reproduce problem:
Remove `find ...` call, use `cat somefile` insted, don't use directory traversal. Minimize the code so it don't do anything unrelated to fork.
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