Why would the list run only on Linux?

[DoNoHarm]

You are right and the md5sum was not identical. However, now the md5sum is identical and the word count before the cracking process is the same, but the problem persists. So here is what is happening:

1 - Some of hashes are already cracked using over-the-internet lists
2 - Made new list in The-Distribution-Which-Does-Not-Handle-OpenCL-Well (Kali) and copied it to windows machine, md5sum is identical
3 - Started the crack using the new list on The-Distribution-Which-Does-Not-Handle-OpenCL-Well (Kali), everything is good.
4 - Started the crack using the new list on Windows, not good. Candidates are shown in the previous post.
5 - Double checked the md5sum of both the hashes list and wordlist, still identical
6 - Added a new stdout line and now the batch file looks like:

Code:

hashcat64.exe -m 5500 Hashes.txt collection3.txt --stdout
hashcat64.exe -m 5500 Hashes.txt collection3.txt

7 - The stdout shows the correct list and is the same as the stdout in the The-Distribution-Which-Does-Not-Handle-OpenCL-Well (Kali) machine
8 - When the cracking process starts, still the same problem! The words on the list are not used as candidates.
9 - I thought maybe they are used but not in the candidates column because the list is too small, so I added dive's rule to take a longer look at the candidates but still the same problem.