Hi,
this could be caused by Autonomous CAN biasing. The device only terminates its CAN bus pins to GND while
- the CAN block is in a low-power mode and
- the bus is idle for longer than approximately one second.
Otherwise the CAN bus pins bias towards 2,5V.
Each time there is traffic on the bus (see Fig 9) an internal timer is reset and the bus pins bias towards 2,5V. At bus silence the timer starts counting until about one second. After this silence time the bus biasing changes towards 0V.

So the first frame is not probably received without error due to GND biasing and also makes bus biasing to 2.5V again.
Then if second frame is received within about one second, the transceiver wakeup normally.
See TR1309 Application Hints - High speed CAN transceiver for partial networking TJA1145 (http://www.nxp.com/documents/report/AH1309_v1_1_Application_Hints_TJA1145.pdf) for mor info about this transceiver.
BR, Petr