Ive flashed the 1.2 controller update and things seem a bit better for me so far, previously i was seeing the second pga only producing 50% accepted shares compared the first pga, tested over multiple 12/24/48 hour runs, i.e.;
so far (after only 10 mins or so) both pga seem to give the same number of accepted shares;
ill report more when its been running longer.

after 13 hours, not a massive difference from before;