Oh God yes, the bloody JET Japanese Beginner course is all romaji and it drives me crazy. Couple that with the weird grammar points and it's just not worth doing - I just study with Genki (my JTEs help with the Osaka-ben) and just muddle through the JET tests.
Seriously, how can a Japanese course for people who are guaranteed to be in Japan not use furigana, and/or the occasional kanji? It starts three or four months into the job fer crying out loud!
Seriously, if you get over here don't bother signing up for the CLAIR language course, it's a major waste of time.

A note or two on Genki - it's really good as far as texts go, but it does sometimes teach textbook Japanese. Generally people here don't use some of the words in the book (i.e. 話す hanasu for 'to speak (a language)' - people on the ground actually use しゃべる shaberu 'to chatter'), and it's all Standard Japanese so if you make it over here on JET there'll almost definitely be some regional differences in your hometown. People will still understand and be able to use Standard Japanese just fine (it's the official national language, and is used for keigo or polite/formal speech), but most places here have their own regional dialects which can be a bit or even quite different. I came here with no Japanese whatsoever besides the usual 'konnichiwa, sushi, etc' words everyone knows, and now I'm learning both Standard and Osakan Japanese. As Goki can attest, the two can be pretty different.
Osaka-ben is better, obviously.