I've had similar issues with my 5EAT, I was out in the middle of nowhere at it just started thunking when trying to change down (or up), eventually got it back to Winger in Hamilton and apparently it was the valve body. That's been replaced, but I'm not 100% sure it's fixed,.
My mate has the same car and had the same issue, he had the valve body replaced as well, but after a couple of months it started again and he ended up with a full gearbox rebuild.
We're both lucky we've got mechanical warranties, otherwise the valve body replacement is ~4k and I don't want to know what a gearbox rebuild costs, could be cheaper to just convert to 6sp and cert it.