That is not a "weirdo" thing, it's actually a shy, submissive reaction. You are right in that she has taken to seeing the desk as her "safe place" but den behavior is common in shelter dogs.
Makes sure you not sitting directly in front of the desk if you are trying to coax out the doggie. That blocks his access and will probably make him uncomfortable. Give him plenty of time to come out on his own but he needs to go potty, so you might try standing to the side and throwing out something tasty in front of the crate.
I've copied an article that might apply to your situation, but you may need to extrapolate a bit.
La Trenda, MA, MHR
Puddin's Training Tips
SAPAWs, San Antonio Express News City Brights
Unsocialized Dog Tips
(These tips also apply to well-adjusted, happy, friendly dogs)
Applies to your own shy dog, a shy dog you meet on the street or volunteering at a shelter.
* Caution - although a shy dog's first response is mostly likely to run away when frightened, a shy dog can and will bite if she or he feels cornered or trapped. Give yourself and the dog an escape route when socializing.
How do you recognize an unsocialized dog? One, some or all of the below:
Eyes darting and/or wide open
Backing away from you
When the kennel worker takes me out of my kennel and hands me to you, please just let me walk. The first thing I want to do is go potty. Then I want to smell where everyone else has pottied, then I want to stretch my legs and get used to the idea that a stranger is walking me. If you try to pet me as soon as I come out of the kennel, you will probably frighten me; I will feel trapped and forced into getting petted. Also if you try to comfort me when I’m scared you only reinforce my timid behavior.
Please realize that we don’t have to do anything when we are together. I’m just happy to get out and about. Don’t feel bad if I don’t want to play fetch or jump in the pool or talk to you right away.
If we are in a play area together or a kennel or a house, please give me plenty of space and allow me to come up to you when I’m ready. I’m much more comfortable meeting you on my own terms. I will warm up to you much faster if our meeting isn’t forced. Let me come to you when I’m ready.
Please don’t make any sudden movements. All movements should be slow, flowing and deliberate. Let me know what you are doing at all times.
I feel much more comfortable when we are on the same level. I would really appreciate it if you would sit on the ground or floor for me. Then you don’t look so big and you look much less frightening.
Please don’t look directly at me. Use your peripheral vision if possible. In doggie language, a direct stare means that you are challenging me and looking for a confrontation. Try to keep your side to my side.
Please don’t try to pet me on my head. This can be frightening to me. Once I’m ready to get petted, I will approach you. When I do this, then slowly raise your cupped hand (no straight fingers) towards my chest or shoulder and give me a little scritch. If I don’t cower, then you can try scratching my back. If I try to run off while you are petting me, please let me. I’ll come back when I feel more comfortable.
If I'm frightened, it's best to leave my leash on at all time when we are outside. Even in an enclosed area like a yard. If not, you might have a hard time releashing me or getting me back inside.
What happens if you can’t pick up my leash or get my leash back on?
Please don’t chase or corner me. This will only frighten me more and I might try to bite you
You might want to try hiding the leash and just petting me first; then slip the leash on when I’m not expecting it (slow and deliberate movements)
Since I’m so timid, I might try to escape the first chance I get. If I get loose, please don’t chase me or corner me. This will only frighten me more. Call softly if it doesn't seem to bother. Try walking or crawling backwards towards me. This make me more comfortable.