i think you sort of answered your own question, having to use the cube. It sounds like an impedence issue. I've had similar problems with lapsteel, dobro, and sometimes even just really old (but awesome sounding) guitars. What are you using for an audio interface? I use a preamp with a MOTU 828, and i've found that if i'm dealing with a weak signal, it's important to boost things up evenly between the preamp and the interface. A weak signal definitely affects tone, and a signal boosted too much at one gain stage will be even worse. Using the preamp, i can always get lots of signal. If you don't have a preamp, and don't care to buy one, i would recommend a really good direct box. Two that come to mind are the PRS guitar interface, or one of the many Radial boxes. The Radials can be a bit expensive, but if you're running direct into logic without an interface, it would for sure give you much better results. If you are running without an interface, and doing any even quasi-serious recording, i'd also recommend getting even a cheap external interface to get your signal away from the super-noisy low grade audio components and all the other noise-inducing stuff in the vicinity of the audio input. Particularly on a laptop.
