Roku OS 10.5 was announced a while ago, but I haven't seen it made available to any device I own (so, I'm assuming it hasn't been released). Hopefully, this fixes issues.
I personally don't have that many video files on my network, but I just converted my audio to OGG format. OGG is every bit as good as AAC at higher bitrates (so, it's comparable to AAC-LC). I setup a batch script to covert all audio and just let it run until it was done (audio encoding is relatively fast, so it didn't take too long).
That fixed the issue for me... but as other's have said, letting a problem like this persist is just a large incentive to go to a competing device.