I sold some ether through bitsquare, and used quorumwallet. It sends the funds by executing a smart contract. The transaction is visible on the block explorers as internal tx, and the balance adds up correctly. But the receiver didn't see it in his wallet, and claims he cannot spend it. Is there a better tool to check this claim than etherscan.io or etherchain.org? The account has about 90 transactions.
There's no practical difference - ether is ether, regardless of how it arrives. Value transfers made by contracts won't show up as separate transactions, though some block explorers are capable of showing them, either associated with the original transaction, or associated with the account that received the transfer. ether.camp has a more comprehensive view than most.
'Bare' accounts can't show incoming transfers in general because of the above; the usual recommendation is to have a wallet contract if you want to be able to view incoming transfers.
I have found that ether.camp and etherscan.io should be used whenever you deal with contracts / transactions to and from contracts. Blockchain explorers must implement a way to read contract transactions, which requires a bit more than standard transactions. Some do it better than others.
I would also recommend when sending ETH to a third party that may or may not be 100% familiar with ETH, it is best to send it to a standard account and then send from there (for the time being).
There is no real risk in sending from a contract, beyond the obvious hassle and necessary communication with support representatives to get it sorted it.
It's also worth educating whoever you are dealing with. For example, ShapeShift's support team used etherchain in the beginning until they started encountering the same issues. They now seem to use etherscan to verify transactions as it gives a much clearer look at transactions, internal transactions, and especially errors in contract execution.