ZMQ Raw TX doesn't include all transactions
There is a limit of how many messages can be in the ZMQ:

http://api.zeromq.org/2-1:zmq-setsockopt


  The ZMQ_HWM option shall set the high water mark for the specified socket. The high water mark is a hard limit on the maximum number of outstanding messages ØMQ shall queue in memory for any single peer that the specified socket is communicating with.


So you might need to specify the option -zmqpubrawtxhwm to something that is larger than the default of 1000.