Hi @1115,
See this post. Kingdom-level classification is almost always due to using the wrong reference sequences/classifier for your sequences. If you are sure you have 16S query sequences and a 16S classifier, the issue could be non-biological sequence (e.g., adapters) attached to your sequences.
Nothing is wrong with the pre-trained classifier. This is either a problem with your data, or just that the sequences are a different marker gene.
You will need to use different classifiers for different projects if they use different marker genes.
I hope that helps!