Why was I only given a 3-month Non-O Visa instead of the 12-month I applied for?

There is no 12 month VISA inside thailand 🙁 I think you don't understand how the process works

You FIRST apply for a 90 day Non-O visa for 2000baht, that goes under review for 2 weeks, then you go back to get the Non-O visa and a new 90 day stamp inked in

THEN you wait

until you have 30 days or less left on that 90 day stamp, get all new documentation, bank letter, TM30, lease, updated bank book, TM7 application for extension form, etc and go back to apply for the year "extension of stay" for 1900baht on the 90 days you got

They will take your application and you pick your passport with the extension in it up the following day

After that IF you need a re-entry permit to get in / out of the country the coming year you buy one (single re-entry 1000baht, multiple re-entry 3800baht)

And yes, every time you apply you will have to provide the forms, bank stuff et al.

Are you sure you did not apply for an in-country Non-O VISA as a prelude to applying for a 12 month EXTENSION OF STAY?