There are a couple of things I can think that could cause the problem, it will help to know what format the books you are reading are in. (i.e. KePub synced direct from Kobo or sideloaded with Calibre's KoboTouchExtended driver, or ePubs sideloaded without using Calibre or using Calibre's default KoboTouch driver.)
The KePub reader will try to substitute any missing glyphs in the selected font with glyphs from another font, so if the fonts you have sideloaded don't have Greek glyphs then you will probably see glyphs from one of the standard fonts, which could explain why they don't change.
The ePub reader allows the publisher to override the font from the book's stylesheet, which prevents that font being changed from the device. If that is the case then you would need to change the book's stylesheet to fix the problem.
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