Great. Thanks for the additional information. I really appreciate it.
Of course, the first thing we should always do in these cases is start with a trip to the vet to make sure that she doesn't have something like a urinary tract infection going on. Things like that in a female dog can result in a break in house training, so ruling that out should always be the first step.
Then, if that comes back clear, I think if this were me, I'd attack this a couple of ways:
First, since you think that she's a bit nervous and this behavior only seems to rear it's ugly head at night when it's raining, I think you could try using an over-the-counter product to help take the edge off her anxiety.
A couple things you could try would be:
Melantonin is an over-the-counter drug that can be used to treat some anxiety issues in dogs. The dose you would give would be up to 3 mg given orally whenever necessary up to every 8 hours. More information can be found here: http://www.petplace.com/drug-library/melatonin-melatonex/page1.aspx , which includes risks, warning signs to watch out for and other bits of useful information.
Try a DAP collar. These are collars that are impregnated with a man-made version of the dog appeasing pheromone, which is a pheromone that nursing bitches give off to their pups to help them feel calm and secure. It's something that humans can't smell, but it has an amazing effect on dogs with anxiety and other issues. Although you can find them at your vet's office..you can also find them online at places like Amazon.com and Ebay for much cheaper. Just make sure they're DAP brand, as they seem to work better than some other versions.
Next, instead of allowing her to sleep on your bed, since she was crate trained at one point, I'd get her a crate to use at night. You can put lots of comfy blankets/pillows in there and even have it in your room, but it gives her a small, den-like space to spend the night. This might give her some comfort plus dogs tend to avoid using the bathroom where they sleep, so keeping her in a crate may help break the habit of urinating on your bed.
Since this sort of has a history of happening in the past when she's scared of something, I suspect that using the DAP collar and having her sleep in a kennel will do the trick.
I hope thishelps.