profs are generally used to writing multiple recos. you can tell your profs in advance that you'll be needing 12 copies (so they'll frame the letters accordingly). i don't think you should worry too much about it (since you don't really have an option).
you are not allowed to open the recos! (besides when you ask for 12 letters your prof will want to know which those 12 schools are) i don't see how you'll end up with an extra copy.

only 12 schools?

lol....12 is too few???

CFSO .. have you looked up the cost of how much each application package cost????????
I mean if you can handle 12 application then you are definitely amazing and rich or just very unsure what you want out of your graduate school.
I applied to only 4 graduate program and it has already cost me over 600 dollars for the application process.
Cost break down:
3 $50 per application (nonrefundable) + UPenn costed me $70 because its an Ivy.
$140 to take the GRE (you are only allowed 4 free reporting and I think its $10 for an extra school..correct me if I am wrong though)
$100 for GRE prep materials (use the free stuff if you can from ETS but it doesn't help if you are really weak in verbal or math)
Another $200 for good card stock paper for portfolios, binding, and computer usage (the last part was because I got stupid and couldn't use the paper I bought to print on the laser printer at school so had to go to a print shop to pay to print out the material myself at self serve.. (btw. if you aren't able to use InDesign or Illustrator .. good luck at the cost it will take for them to print out those portfolio for you the way you set it up.)
I didn't add up the cost of shipping out my packages since I had to airmail my next day USPS to get them in on time. I think its around another $100. Send it out early and cheap if you can.
So really I spent closer to $800. multiply that 3 times if you are considering 12.
Anyway... I had to deal with electronic recommendation letters versus print also. My professors and boss were very accommodating. I let them know ahead of time what schools I will be applying to plus gave each of them a package nothing the requirement for recommendation letters. Please pick your recommender accordingly. If they are not good on the computer then just ask them for the print ones. I asked 4 different people to write recommendation letters but in different combinations so that they are not going to get confuse who they are sending it out to.
Also they gave me a copy for my file without me asking for it. Actually I had to try not to give the same "Thank you so much, this is the best recommendation letters I've received speech."
Last piece of advice.... Research accordingly the grad school you are interested in. What do you really want out of the whole program, why would you spend money to go to this school, and if I do get accepted and I decided to go, what are the opportunities available after I graduate. This will save you time and money since most grad. school have different structure in their application process plus they all want the portfolio in different format or size (ie. Letter size vs. A4 and some want it on a CD now)
I narrowed my school down from a list of 15 schools to 4. One Ivy, two great art schools, and local univ with good local connections in the design field.
Good Luck

Well....part of it has to do with my increasing uncertainty over chances of acceptance......I am taking a huge risk here applying from a non-arch background right after graduation. So at the very least I have to make sure I am going somehwere next fall...instead of living in my parents house basement.

If you are applying for 2010-2011 entrance, you have sufficient time to prepare a portfolio. Since you are applying to a MArch 1 program, your portfolio requirement is to demonstrate your creative ability. They mostly want to know if you have the stuff to make a great architect. Although I will be graduating with an interior design degree, my portfolio doesn't consist of all my floor plans and architecture project. I do have one or two in there to show them that I am able to draw a plan properly and synthesize need into functional space but 80% of my project came from my art, photography, and drawing classes. Applying to a massive amount of school will not increase your chances if the content is not applicable to the profession.
Look at the state universities in your area, or look further out.. I know Pratt/Parsons in NYC doesn't require you to be in the architecture field before entry. If you think you have a chance then apply to an Ivy like Columbia where their MArch program cater to non-arch major..
Take some architecture history class and some type of art class you enjoy doing. Also figure out why you want to be an architect. This is a great subject to write about in your statement of intent. You have to realize that this is not a money making profession. It is more of a passion. Beside, I would kill to have a great school that I want to go to and be able to live in my parents house for free.

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Beside, I would kill to have a great school that I want to go to and be able to live in my parents house for free
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I'd very much agree......^___^