The 3% Quidco cashback rate from Greater Anglia started in about November. I've had 9 transactions track since then. I don't remember any that have not tracked, but none of them have paid out yet. The site says that they take 8-12 weeks to pay out. I've had 23 Transpennine Express transactions. The ones up until October 2nd have paid out. The ones after that are still only tracking.
I had a load of transactions with East Midlands Trains which didn't pay out for a year. I contacted the Quidco support by the online chat, and they paid them out for me.
I keep a closer eye on Quidco cashback for hotel bookings, as they are higher value than my ones for train tickets. For Expedia bookings, they say that the payout is 13 weeks after the hotel stay. If I have transactions that haven't paid by then, then I contact the Quidco support, and they usually pay them.
I normally use Chrome with an advert blocker for day to day browsing. When I am going to use a cashback site, I switch to another browser, without an advert blocker. It means the cookie from Quidco/Topcashback won't clash with one from my earlier browsing. Advert blockers can also get in the way of the referral links.
Similarly when there is an extra bonus cashback, I make a note of the Quidco ID of the transaction that I used for it. Otherwise it can be hard to work out which order matches to a bonus transaction a few months down the line.