Not sure. Could you zip up the project and email it to ezra@embrio.io? I can take a look at it tonight.

Oh I didn't realize it was so simple. It looks like your arduino program has no wait so the digital read happens constantly. Try raising the refresh rate of your agent. Or try using an interrupt agent. It has one digital input node that fires on an interrupt instead of on a timer. A regular node fires on a timer at the set refresh rate, so yours is probably doing 32 digital reads per second which is missing your signal.

The architecture of an Embrio program is that you have nodes organized into agents. Each agent has a refresh rate (in the bottom right of the screen), and all of the nodes in the agent update that many times per second. Your Arduino program does a digital read, and then doesn't wait at all before looping again, so it's doing a huge amount of reads per second, so it's able to catch all of the changes on your pin. On Embrio it's only doing about 32 reads per second (or whatever your refresh rate is), so your pin is changing faster than Embrio is reading. So you need to use an "interrupt" which fires when the pin value changes.

There are two things to try.

First you can use an interrupt agent. I just noticed there's no documentation for this, I'll add it soon. Right click on a folder in the tree and select "new interrupt agent". This agent has a special input node. Pick your pin and set the interrupt type to "change". The trigger will fire whenever the digital pin that you selected changes. You want to have as few nodes as possible on this agent, maybe just a counter. Make the counter's output external (by clicking on the little plug icon next to it), and read that value from a regular agent.

Also you can try writing interrupt code right in a custom Arduino node, like in this example of using a rotary encoder.

Let me know if that does it!