We had several more non-confirmed ZEC-transactions, so we've initiated a new investigation on the issue and had to stop the payments for a while.
The results are:
1) Our previous assumption of fork-transaction was incorrect. Balance of that transaction was restored to accounts.
2) Transactions were silently refused by the network, but the wallet was still waiting for it. That happened after increasing the maximum number of tx outs to 1500 in the desire to reduce transactions count and the wallet size growing, as was suggested by the developers here: https://github.com/zcash/zcash/issues/1749
3) We had to reindex the wallet to restore proper balance, but it broke again after restarting the wallet... so we've moved to the new wallet again and split mining wallets from paying ones.
4) All the rejected transactions were unrolled.(Transactions removed, balances restored).
5) Payment system was updated and payments were executed.
We are really sorry for not having time to answer all the mails and messages at forums, as we were trying to clear the situation and fix the payments as soon as possible.
We've increased the mininmum payout limit to 0.005 ZEC to decrease the number of transactions.