You might try adding:

$File::Find::dont_use_nlink= 1;
[download]

near the top. This bug in File::Find existed for many years even after I complained about it. The most recent File::Find claims that it never causes a problem, but all of the previous versions also claimed that when it clearly wasn't true. (:

Your problem description doesn't match what I'd expect if this were the problem, however. Your problem description sounds like a bug in File::Find (like it is not properly clearing out some remembered state from the first run). But that is just a guess as well.

If I had this problem and cared about getting File::Find fixed, then I'd use "perl -d" to see why the second run is stopping early.

Even more likely, I'd just replace File::Find with about a dozen lines of fairly simple code, for example, Re^2: aborting File::Find::find (gotchas). :)