Do you directly connect the iPads headphone jack to your sound card's line inputs or is there a way to stay 100% digital? The inherent DA/AD conversions happening over a shitty 3.5 mm stereo jack in this scenario probably degrades the sound quality quite a bit and the iPad's headphone jack DA converter probably isn't very good in the first place.
I know some apps allow you to export loops and import them via iTunes but IMHO this is a workflow killing, intuitive pain in the ass.