There is a Kobo desktop app. Might be worth having so you can check it before it is sent to a device.
You may be suffering from non-breaking spaces which Sigil will put into your text. Use search and replace to pull them all out before saving. You can always put them back in those few cases where you need them.
Also, drop caps, if not done well, can cause odd behavior in my Sony.
You might compose a test epub for checking and throw in the kitchen sink....one item at a time, then observe in the reader app. Maybe you can track down what is causing a problem. Take your stylesheet from your problem child and copy each line into your test epub one at a time until it goes bingo!