I wish I had an answer because I am experiencing something similar here. Though in my case my kitty still cries even in my lap. She doesn't like to be held, which has always been the case. She used to be very quiet only crying when going into heat. I had her spayed last week, and the procedure did not go smoothly. She had cysts in her reproduction system and she had severe swelling, so the vet had to cut much more then he had to with either of my other cats. He decided to take her home with him that night to watch over her just in case, since the stitches didn't quite take and there was quite a bit of bleeding. She spent the night with him, came home to me the next day.
With the antibiotics we have given her she has recovered very fast. She is in good health now. But now she doesn't stop crying. She goes into the darkest corners of the apartment and meows until I come and find her. Then she stops for five minutes and continues crying.
I am not being driven crazy by the meowing, but I am curious by it, especially since it doesn't seem like anything I do makes her feel better. The vet says that she is in good health, if not a bit overweight (something that surprised me), so I am left with something of a situation. I can perhaps make a guess of what is bothering her (she never left the apartment for extended periods of time and then we had to keep her in isolation for two days while her belly healed up before reintroducing her to Isis and Niko so I can't imagine that was any help to her simple kitty head), but some assistance as to how to comfort her would be greatly appreciated.
Thought I would add this with CatMorris's thread since we seem to be experiencing the same problem, just different situations. (no sense in creating multiple threads.