Man, that sucks big time. Really. From your post I assume you haven't been regularly updated about the qualification process, meaning they haven't informed you about the budget cut (I was informed at the beginning of November) and whether you have been spared by it (the news was out in Poland at the beginning of December). If so, perhaps they're clumsy with their paperwork and asked you for documents they had no need for (in Poland, December was the final deadline to deliver a graduation certificate for those who passed the second screening) and your academic advisor was misinformed as well, but wanted to sound reassuring? Not that it changes much, but it might be an explanation for what actually happened.
Well, that's a reasonable hypothesis. Today I received an e-mail from my academic advisor in which he said they were extremely surprised to know that many applicants who were clearly accepted by the universities were ultimately not allowed to go to Japan. Also, he said that the reason for such issue must be somehow connected, again, to the reduction in MEXT scholarships due to the budgetary cut, and informed that even themselves were yet waiting further detail from MEXT and Foreign Ministry about the selection that took place regarding this situation.
Besides clarifying that my denial most likely did not occur due to my performance or documents (a relief, actually), he also stated that we should all expect the selective process to become stricter from now on.
Well, it sure lightens up many things, since, apparently, it had nothing to do with the applicants, embassies, universities or advisors, but with the procedures which took place inside MEXT regarding the new budget policy that was planned by japanese government. Confidential stuff, I guess.
That being the case, well, bad luck.
Not willing to be a buzz killer here, of course xD, but I'd like to know if anyone else failed to succeed in this same manner as well. I believe that when receiving such an unexpected result (yes, a hell of a sneak attack, I might add) people would just stop wandering around the forum in grief, but if there is someone like me out there, please let's desperate together, haha. And, of course, start our plans of revenge for 2012.