Hopefully this will improve with time. I think it's paramount to concentrate on each pair within the Triad. Make 100% sure she's getting all the one-on-one quality time with both Tom and with you...so that when you and Tom are together, it just seems more natural. (Everyone needs a little alone time and she's surely eventually gonna want some as well, thus giving you and Tom a good opportunity.)
If she's had no trouble falling in love with you, then I don't think she's struggling so much with the concept of polyamory....but it's more like she just has this innate instinct of jealousy/envy that's been ingrained in her head like every other person in the world raised in a monogamy-oriented society. Unfortunately, she's just having a harder time getting over it. All three of you need to work on that...as well as other trust-building work within the group.
I'm not ashamed to say it...we actually had to go to a therapist to discuss this issues in our early days of our triad. (Make sure it's a counselor who's experienced with polyamory!). It helped a good deal.