Another possibility is that the /g/ is being lenited into a voiced velar fricative /ɣ/, as is common between vowels in Japanese. (See "Handbook of the International Phonetic Association: Japanese" by Hideo Okada, or Wikipedia.) Further, since the second /g/ has rounded vowels (/o/) on both sides, it is likely to be somewhat rounded (/ɣʷ/ = /w̝/).
The utterance, phonemically
/aɽígatoogozaimásu/
then would be something like
[àɽíɣàtoow̝ozaimás]
Judging by your username, I'm guessing you're a native English speaker. Since most varieties of English diphthongize /o/ to something like /ow/, and minimally distinguish vowel length, English speakers are likely less sensitive to the intervening [w̝] and to the extra-long vowel sequence /ooo/. So you hear the utterance as
/arigatoːzaimas/
which would be transcribed as "arigatōzaimasu".