My guess is that you haven't seen the tweak 'save_template_title_series_sorting'. It could be the source of your problem, but as you don't give any concrete examples, I can't be sure.
The tweak documentation is:
Code:
# Control how title and series names are formatted when saving to disk/sending
# to device. If set to library_order, leading articles such as The and A will
# be put at the end
# If set to 'strictly_alphabetic', the titles will be sorted without processing
# For example, with library_order, "The Client" will become "Client, The". With
# strictly_alphabetic, it would remain "The Client".
save_template_title_series_sorting = 'library_order'