[Edit] I changed the title of this subject to more accurately reflect the content of this post. I am a follower of Buth's "Restored Koine" or "Imperial Koine" pronunciation. I'm an American, and don't always pronounce my υ and οι as [ÿ], but I try. I use Buth's pronunciation scheme becuase it is the closest to NT pronunciation that you can get. I have no desire to use spell-talk, as I am involved in the communicative approach to teaching ancient Greek.
I listened to Buth's audio of the 1st John passages that you cited. You are struggling with two things.
First, Buth's audio is read at conversational speed; but in some instances he reads a little slower, or will speak two words which could have been pronounced as a single word (using elision if spoken faster) as two words, sometimes for emphasis. When someone is speaking at a conversational speed, they do not insert pauses between the words. So in some cases, you are hearing a continuation of the vowel from one word to the next with no pause. In written poetry (and songs), there is usually an apostrophe marking the elision, e.g. ἐὰν δ' ἐν = ἐὰν δὲ ἐν (1 Jn 1.7). That's how Buth reads 1 Jn 1.7. One person's reading of 1 Jn 1.7 may have elision, another, slower reader who pauses on every word, would have no eliding of vowels.
When dissimilar vowel are pronounced in succesion: e.g. φωνὴ ἐβόησεν, your mind ignores the transition. The change from one vowel to the next is a sort of glide sound - one continual range of vowel sounds with some intermediary pronunciation which does not approximate either vowel η or ε. But your mind/ears hear the two distinct phonemes.
In English, as I believe happens in Greek, if someone pauses quickly between words, they are actually pronouncing a glottal stop [denoted by the IPA character [?] (without the dot). (In English, the feature is represented, for example, by the hyphen in uh-oh! ) cf. Wikipedia: http://en.wikipedia.org/wiki/Glottal_stop
. The glottal stop is not a written consonant in English, but it is a consonant that is spoken (and unwritten). Now one could just stop pronouncing a vowel, but that takes a little longer than using a glottal stop. You may be hearing a little of both.
In some instances, e.g. *1 John 1:6: ". . . αὐτοῦ καὶ ἐν τῷ σκότει, for clarity there is a slight pause (or glottal stop) happening between [kε] and [εn], so as to make the phrase more clear. This pause can be quick (which requires a glottal stop - or some form of a glottal stop) or slower (simply letting the airflow stop).
I would say that Buth uses a glottal stop in 1 Jn 1.1 καὶ αἱ χεῖρες ἡμῶν.
Secondly, The point is that people do not realize how they pronounce their own language. And so variations, which are not phonemic [meaning associated differences] are ignored and heard as being the same sound. You wrote
It sounds too sloppy.
Have you ever closely listened to a recording of yourself in English? In English, we enunciate the letters L, T, K, etc. differently, but we hear them as the same phoneme. If you ask the normal person on the street if there is a difference in pronunciation, they would say "No way man, I pronounce every letter the same all the time." But when you repeatedly listen to any audio, in any language, you will start hearing variations of which you were not originally aware existed. What you are struggling with is the fuzziness that happens in spoken language. The more you listen to Greek audio, the less this will be a concern.