The way I understand it is that the phrases aren't really any different, but in the negative form 分からなくなってきた is much more natural. ように is inserted in the positive version for practical purposes. ように means "so as" or "as if" when translated into English, but it also serves to turn verbs into adverbs. That is what is happening here. 分かるようになってきた means "I have come to understand." Since the verb 分かる can not affect the second verb なる at the end on its own, you add ように to turn it into its modifying adverbial form. In the case of the negative version, the negative form of 分かる is 分からない and it can already be changed into an adverb by changing 分からない into 分からなく, which is the adverbial form. All verbs and can do this in their negative forms, but not in the positive. For example: 雨が降っているので、外で運動できなくなってしまった。 Since it's raining, we can't exercise outside. 突然雨が止んだので、外で運動できるようになりました。 Since the rain stopped, we are able to exercise outside. Does all this make sense? I hope its a bit more understandable now. Let me know if you need any additional explanation. :D