Thanks for sharing!
This one stumped me for a while because your files look fine to the naked eye, have the same number of entries, etc, and I don't have your query sequences to replicate the exact error you have.
But I believe I discovered the problem:
Your fasta file (but not your taxonomy file) contains invisible special characters (^M) at the end of the accession #s (this is a windows newline character). vsearch seems to be interpreting this newline character as part of the accession # and hence there is a mismatch and so much chaos. You can use something like dos2unix to convert your fasta file, and then everything should be okay.
Please give that a try and let me know if it works!