There are very few rabbits that actully enjoy being handled. They are a prey animal and consequently being restrained by a predator like us is quite stressful and their instinct is to escape. Its great that she is so friendly the rest of the time. I assume you know how to handle her correctly such as holding her firmly under her front legs and rump and holding her close into your body. Talk to her and reasure her constantly. The other option may be to avoid he stress of having to handle her (unless it is absolutely neccesary) by training her to climb in a box so you can take her to her run.

Good luck

Lambchop