Twilight was not just an avid reader of books. Coming to discover that Manehattan had a publisher that networked and distributed scholarly journal magazines from all walks of life, she had taken to their subscriptions--all of them, and was currently reading one about psychology. It was tied with her study of friendship, as it was dealing with a discussion on trust. It was a long read, but the generalized idea of it was that being invited to spend time in another pony's house and then bedroom was a sign of trust, and the elaborate on a theory and several other models of psychology that tied with it. It mentioned that the level of trust it showed was different from pony to pony. Some ponies trust easily, and let new friends into their homes easily. Others are harder. It also acknowledged that a pony can be warm to strangers and friends without necessarily taking this step of trust and inviting friends into their homes.
It interested Twilight because, as she finished it and considered the material, she realized that she'd been in everypony's homes, including Fluttershy's... but not Rainbow Dash. Out of her friends, Rainbow Dash was the only pony who hadn't invited anypony else into her home that she knew of, aside from Gilda, who had been a friend in school...
Rainbow also knew that Twilight could walk on clouds now, if she wanted to, so considering that loyalty and trust were very different things fundamentally, she started wondering if Rainbow trusted her a lot or not. Oh sure, Rainbow would trust her with her life, she figured, but Twilight didn't know just how much Rainbow could trust other ponies with her emotions and feelings of insecurity, which she hid well and sometimes dangerously so... Twilight hadn't forgotten Rainbow's panic attack in Cloudsdale.
On a side note, Twilight's article had referenced some old folktale about a powerful fairy pony who was sick from a germ, and had to trust an Earth pony to shrink down, enter her, and remove the germ. The fairy pony had been mistrusting, but had eventually allowed the Earth pony to enter her, not to save her life, but because she grew to care for the Earth pony. Twilight had of course read this same folktale and found it charming, if a little weird.
Twilight decided to visit Rainbow Dash. She left a note for Spike to tell him where she'd be while he was out doing errands for her. She stepped out into Ponyville and started trotting to the outskirts, where Rainbow's cloud home hovered near the roadside. She looked up at it and smiled.
"I bet she'll be surprised!" she said and then cast the spell on herself that would enable her to walk on clouds. She then broke off a small chunk of the cloud with her magic and levitated it down to ground level, stepped on it, and then levitated it back up to Rainbow's home and nudged it back into place. She trotted along the soft cloud surface and approached Rainbow's home. She knocked on the door.
Nothing happened, so Twilight knocked again loudly, and waited. Frowning, she began to wonder if Rainbow wasn't even home before Rainbow peaked her head out of a high window. "Twi? What on earth are you doing... up here?" she asked. Her voice sounded funny. Twilight wondered if something was wrong.