I think the "neglect" part may be due to miscommunication. I think that Yuna's mom thought that IMG Korea was not doing enough in terms of helping Yuna get sponsors. I seem to recall that, when questionned about it, IMG Korea replied something along the lines of Yuna not being marketable or something like that. The bottom line is that IB had a much more appealing marketing/sponsorship deal.
That's where the tension with IMG Korea started. It was supposed to be resolved by having Yuna skate in the IMG show in 2007, but that got canceled due to the fire. According to yunaforum.com, IMG Korea put Yuna front and center in aplogizing about the cancellation and made it look like it was her show, even though she was a last-minute addition. And this is why some of her fans feel so strongly about IMG Korea.
Again, I think it is Yuna's mom trying to say something PC to the media. I do not think there was any argument with IB. Her contract expired, and it would be great if Yuna had a little more control on her commercials/sponsorships...etc. What IB did with Yuna was amazing, but it was bordering on over-exposure, IMHO. Just judging by the number of appearances she did in the last month, I don't think the poor girl got a minute to herself... and this is when she was supposed to be on vacation, relaxing and trying to decide her future. She does not need all that exposure anymore, and having her own agency will help her tremendously in that regard. Besides, she's always said she wanted to support the junior skating program in Korea (she's already sponsoring some junior skaters), and having an agency with her name on it that could sponsor them is a big step in that direction.
Honestly, I think Yuna is done competing. I would love to be wrong, but this is my reading on this news.