There is nothing more annoying than BAEC's total lack of knowledge about booking domestic flights on JAL with ba.com...or BAEC staff doing the same over the phone...
I am not sure whether it is stupidity or laziness...either way, it is a total cluster F'k dealing with stuff that can not be booked on Ba.com...or for that matter, stuff that should be bookable on Ba.com and you can get all the way to seeing space only to be denied with Computer says no....
What is fact is that you can book on flights on JAL, JAL express, JTA and JAC using BA miles...so even though you can not book FUK-OKA on BA.com on JTA, you can ring up and if a person puts in effort, you can use your miles...sadly, it takes more than the normal hang up and call back 3-4 times to get the response you want...and even more effort to get the fees waived since telling BAEC agents it can not be done on BA.com regarding JAL flights is dealt with we do not believe you...nice.
problems i have found, i can use ba.com to search for flights from Hiroshima to HND...funny, you put in Hiroshima and ba.com does not know what to do...but then put in HIJ to HND and voila, lots of flights...that said, try booking one...COMPUTER SAYS no....so sometimes, search the exact airport code. that said, i have also found that unless Ba.com recognizes the airport code...for example, book FUK and it competes with Fukuoka...you can see space but BA.com will not allow you to book. same with HDN ITM or NRT ITM...now part of this could be ba.com not working from time to time but i just think ba.com falls down on many JAL flights domestically...
So you just have to be VERY patient...I feel your frustration...also remember, you can only book 2 months out.
Others here suggest there is a good deal to buy tickets etc. with some visit Japan etc. but they have obviously not seen the value in using miles...one little glimmer for me personally after BAEC gave those in NA the shaft on partner awards...
just booked three tickets FUK-HND in Y...price with tax...just over 40,000Yen or 480US$....price with miles 13500 (4500 each) and get this....$5.11CAD in fees total....my child's ticket was only 0.97CAD in fees...less than a buck...and because i am a parasite those miles cost me nothing....well, other than using my trusty credit card for my company expenses...
so be patient. there are ways to extract value for domestic flights...now have to book HND to ITM....and wonder how many calls to BAEC will be required to get this done.