1. Which version is more common?
I have never heard anyone say 'Funny enough' as a stand-alone phrase to show that a situation is unusual. It sounds wrong to me, while 'funnily enough' sounds normal.
2. Or is there any context that one is preferable over the other? Yes.
* If you want to say that something is sufficiently amusing (as @PaulBacon says 'meeting a decent level of humour' ) you would say that it was 'funny enough'. For example, "Should I tell that joke about the elephants in my speech?" "No. It isn't funny enough". NB I presume this is the construction that @Dania is referring to.
* To highlight the fact that you are telling someone about an unusual situation or surprising coincidence, the only phrase I am aware of is "Funnily enough" . In this context, 'funny' means 'strange'. We say "Funnily enough" in just the same way as we might say "Oddly enough" or "Strangely enough". I can see no grammatical logic at all in saying "Funny" in this situation. It has to be an adverb.