If you think it might be partly because she hates being separated from you, do you think it would help to give her something with your smell on it to keep her company overnight, like an item of clothing you'd been wearing all day? Obviously she'll know it's not you, but I did this for Limpet when we had to board her or have her in hospital and I think it helped a little.
Another thought I have is probably just a pointless observation. Cats apparently have these really interesting territorial arrangements. They claim turf chunks, which they patrol - but the turf chunks shift around over a 24-hour cycle. So for instance, if your bedroom comes onto the Patrol Schedule in the middle of the night, you'll have a cat that ignored that same room all day but suddenly Absolutely Positively Has To Walk Through There at 3am. My son suffered from this, and I can't really say knowing why she was doing it helped much with his sleep disturbance. But it was fascinating.
"Hoe sou jy wat so baie reis die wonderlike mense van ons land beskryf?"
En ek se vir hom, "Man, Johan. Die meeste mense is maar lekker zef"
- Valiant Swart