Also plugging your bass/guitar into an amp them using a digital interface to record can also color your sound. You might want to try a different approach by recording your bass directly into you computer via your audio interface and/or using a mic.
Thanks for your perspectives. I'm finding (like many other things in life) that there is a heaping amount of personal preference going on here; which is good.
My preference is to always use my amp when practicing, jamming and recording. For me there's something un-natural about plugging my bass into the interface and hearing what I play playing thru the JBL monitors. And headphones are a no-go, they get in my way too much. I also like the fact that my amp is on the floor and I can stand directly in front of it while playing. Plus I like the rest of the "band" coming at me from across the room. For me there's no replacement for my big 10" speaker designed to push large amounts of low-end air.
I'm sure you're right that the amp and amp pre-set will color what gets recorded. I don't see that as necessarily a bad thing; and when it is bad, I'm sure I can EQ it out with all the tools I have available.