Simulink in external mode with Arduino - Stops at 2%

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Hello.
When I running a model in Simulink with Arduino blocks in external mode - it stops at 2%. Some Times it more that 2%.
I'm sending both through RX and TX at the same time.
Is that the problem or is it a bug?
I'm sending every 500uS from the computer to the Arduino Mega 2560. And i receive every 1mS from the Arduino to the computer.
I'm using Linux Mint and i have Matlab 2016B.
Isin't there a way to run a model in half external mode? The 500uS signal is only from a pulse generator block. The pulse generator drivning a digital output only.
I only want to receive analog values every 1mS.

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