Update on my own TriNet saga. Had the same experience as you. Filed form 843 and sent it off.
After periodic "we're working on it" letters, one year later (the IRS works so quickly), I got a denial. I appealed the denial and after another round of "we're working on it" letters and *another* year, I finally got my money back.
(The good news is that I *did* eventually get it back)
