If you run setgenerate true too rapidly in regtest mode, bitcoind can crash with
/home/ubuntu/install/include/boost/thread/pthread/condition_variable_fwd.hpp:81: boost::condition_variable::~condition_variable(): Assertion `!ret' failed.
This was reproduced with the Linux 64bit gitian binary.
Sometimes it kills bitcoind without a visible asert failure. Sometimes bitcoind just misses the RPC entirely without any visible error and without killing bitcoind.
Setgenerate is marked as 'threadSafe' in the vRPCCommands table. This means that a potential race can happen if it is not really thread-safe. You could try setting threadSafe to false (which will make it acquire all locks beforehand) to see if that fixes the issue.
This is resolved by now. Don't use setgenerate on regtest, use generate.