It could be when you loaded her that she was anticipating pain still. It might take several tries doing what you did today before that works.
If she’s got pain happening in the withers, wouldn’t riding affect it too? I mean, I assume you’ve talked to your vet about it but it seems to me that riding could also exacerbate it if the actual problem hasn’t been resolved.
Anyway, what kind of trailer are you using? Step up? Ramp? Straight load? Slant? Might make a difference in how easy or difficult it is for her to get on or off.