@HHJT,
Would I be right in thinking that these books with the alignment problems are kepubs rather than standard epubs?
If so, you might like to consider using the Kobo Patcher, specifically the patch named `Un-Force user text-align in div,p tags in KePubs`.
When applying the various slider/button changes for font-size, alignment, line spacing etc in the Aa menu, Kobos make use of an internal CSS override sheet in the firmware. Different overrides are used for kepub and standard epub. The kepub one is quite heavy-handed with some of it's overrides, particularly for text-align. It uses
Code:
div, p { text-align: %1 !important; }
whereas the standard epub override uses
Code:
body { text-align: %1 !important; }
where %1 is the button you selected in the Kobo's Aa menu. This would explain why your centered paragraphs are being changed to left-aligned when you press 'Left' in the Aa menu.
The patch I mentioned earlier changes the kepub override CSS for text-align to match the epub one.