Nope, she is not imagining it. My new bike (Trek) has a weird skewer, too, that did not fit right in the trainer. I found out last night, when I almost killed myself upon standing while riding. I'd been on the trainer once before, but the bike suddenly jumped and listed. It did not fall off thankfully, and DH just replaced the original skewer with another one we have.
Kinda scared to use it again, though!