The error message sounds like you need to follow these steps. Basically you need to upload a program from the Arduino IDE, like blink, then close Arduino. Embrio will use the same upload settings as you last used through Arduino. Also be sure to select the correct port in Embrio so it knows where to listen for a connection program.

Sometimes I've also had the hardware error where the serial port is locked and I have to unplug and plug back in the Arduino. I wasn't able to find anything in the connection code that would account for it. Perhaps if more than 1 upload from the command line happens at the same time, like one starts while another is still going, might cause it to get locked somehow.

The slow upload is an issue that I need to look at again. Basically when you do the upload a new folder is created with the generated Arduino code and the needed include files. Then the Arduino IDE is called from the command line to upload. Most of the time seems to be the Arduino IDE opening and configuring. Last time I checked there didn't seem to be a good way to deal with this from the command line. Maybe I can open one instance of the Arduino IDE and use that to upload each time, or maybe there is another cleaner way to upload from command line. I'll investigate more. When I work on an Embrio project I usually do all of the hardware level stuff first, upload a connection program, then do the logic and all of that which usually doesn't require another upload.

If you still have connection troubles after doing an upload from the Arduino IDE and closing it like in the above linked page let me know.

Good catch. I will add to my todo list to log a note when you upload when that option isn't selected. Long ago the default behavior was to put together a command string with the Arduino model selected, but there were some inconsistencies with the Arduino IDE and the naming conventions, so the "use last settings" thing ended up working much better. The Uno BT is just the first Arduino in the list. That list is actually not really used any more, only to group node timing, soon I will remove the list of Arduino models to avoid more confusion.