I have the same problem. I get either a "kicked from server" message or a (slightly) more detailed message containing the error #9006.
So far I've tried:
Using pb files pre-patch.
Using the updated pb files.
Firewall off
Repairing BF3 install
No AV
PB service test (tells me everything works).
Killing PnkBstrA &B and stopping the service before starting bf3 to see if they properly start again(they do).
Here's something that could actually be important though. No pb_(insert command here) commands seem to work for me. I can't create a log file from the console, I also can't seem to create a log file by creating a .cfg file in the actual folder either.
These are the locations of my PB folders(win7 64x):
C:\Program Files (x86)\Origin Games\Battlefield 3\pb
C:\Users\(myuser)\AppData\Local\PunkBuster\BF3\pb
I also have the following files in C:\Windows\SysWOW64:
PnkBstrA.exe
PnkBstrB.ex0
PnkBstrB.exe
PnkBstrB.xtr
ALL of these files were created after running pbsetup.exe(properly adding and updating bf3) and pbsvc.exe
Nothing I see on any forums seem to help me, I really don't know what to do. I could play fine before the patch.