I've found a fix, though it has a knock-on effect.
The fix: Export for cordova like you usually would. Now go into the media folder and what you want to do is replace the existing audio with 48khz (sample rate) versions. How I did this was I fed all my audio through (to change the sample rate you'll have to open up advanced settings).
Now just build in the intel XDK, terminal or however you get it native on your iphone.
The knock-on effect: I've found that on the first play or after the first play in some time, the music just turns into a faint but high pitched buzz. Upon rebooting the app it will all work normally, but as you would imagine this still isn't ideal.
I have noticed that the "preload x" or "preloads complete" doesn't work on ios and I'm curious if this is something to do with it?
Any ideas or suggestions would be great!