If i'm interpreting your code and comments correctly, you are expecting that

    $threads[$i] .= "\n<ul type=\"disc\">\n$link\n</ul>\n";
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will insert 3 (or 4?) new lines after line $i. Whilst this may work, at least some of the time, it is TWWTDI (the wrong way to do it:).

From the Tie::File pod:

Inserting records that contain the record separator string is not supported by this module. It will probably produce a reasonable result, but what this result will be may change in a future version. Use 'splice' to insert records or to replace one record with several.

You should replace that line with

    splice @threads, $i, 0,  
        '<ul type=\"disc\">', "$link",'</ul>';
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Which says 'insert the list (second line above) at position $i, whilst deleting nothing (0)'.

See perlfunc:splice for more details.