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InDesign CS4 ePub export leaves a lot to be desired. This is one of the feature that Adobe has greatly improved as they go along, and CS5.5 (and the coming CS6) ePub export is much better.
That being said, I still have my nits to pick with the export, one of which is putting most of the styling inside of a CSS class instead consolidating into appropriate element rules (body/p/div/ etc...) and using the classes for exceptions. This will cause problems for reading software that use a user style sheet override to provide features such as changing fonts, text color, background color, etc... (i'm guessing this is your 'Sepia mode')
Most of this can be fixed by hand-tweaking the CSS after the fact to do this yourself.
I use a combination of initial generation in InDesign CS5.5, and using Oxygen to hand recode after the fact - however work pays for my tools, and I am generating specific test files to stress readers, so this most likely won't work for you.
For easy generating of ePubs, I've heard good things about Sigil and Atlantis, but haven't had the need to use them myself.
Good Luck
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