Unable to connect to G2 on due SPJS 1.92

I am not sure if this is the right place for this post.

I have flashed a Due with G2 as per the instructions on the wiki. and foing it the first time, it just worked. I got the board executing commands from Chillipepr and all.

Then I wanted to try the jogging widget and everything came crashing down.

Since then, the SPJS has not been able to connect to the Due.

I have erased it and reflashed it, but with no effect.

This is the last part of the server output when running it with -v flag:

2016/10/30 11:53:01 seriallist_linux.go:275: Final port list: [{/dev/ttyACM0 Synthetos TinyG v2 (ttyACM0) [/dev/ttyACM1] 0084-d639-0084-6bd6 ef Synthetos TinyG v2 606d 1d50} {/dev/ttyACM1 Synthetos TinyG v2 (ttyACM1) [/dev/ttyACM0] 0084-d639-0084-6bd6 ef Synthetos TinyG v2 606d 1d50} {/dev/ttyACM2 Arduino Due Prog. Port (ttyACM2) [] 75533343236351E08202 02 Arduino (www.arduino.cc) Arduino Due Prog. Port 003d 2341}]
2016/10/30 11:53:01 serial.go:489: Got metadata on ports:[{/dev/ttyACM0 Synthetos TinyG v2 (ttyACM0) [/dev/ttyACM1] 0084-d639-0084-6bd6 ef Synthetos TinyG v2 606d 1d50} {/dev/ttyACM1 Synthetos TinyG v2 (ttyACM1) [/dev/ttyACM0] 0084-d639-0084-6bd6 ef Synthetos TinyG v2 606d 1d50} {/dev/ttyACM2 Arduino Due Prog. Port (ttyACM2) [] 75533343236351E08202 02 Arduino (www.arduino.cc) Arduino Due Prog. Port 003d 2341}]
2016/10/30 11:53:01 serial.go:546: About to marshal the serial port list. spl:{[{/dev/ttyACM0 Synthetos TinyG v2 (ttyACM0) 0084-d639-0084-6bd6 ef false false [/dev/ttyACM1] 0  [default timed nodemcu tinyg tinyg_old tinyg_linemode tinyg_tidmode tinygg2 grbl marlin] 1.92 1d50 606d 0} {/dev/ttyACM1 Synthetos TinyG v2 (ttyACM1) 0084-d639-0084-6bd6 ef false false [/dev/ttyACM0] 0  [default timed nodemcu tinyg tinyg_old tinyg_linemode tinyg_tidmode tinygg2 grbl marlin] 1.92 1d50 606d 0} {/dev/ttyACM2 Arduino Due Prog. Port (ttyACM2) 75533343236351E08202 02 false false [] 0  [default timed nodemcu tinyg tinyg_old tinyg_linemode tinyg_tidmode tinygg2 grbl marlin] 1.92 2341 003d 0} {/dev/ttyS0 ttyS0   false false [] 0  [default timed nodemcu tinyg tinyg_old tinyg_linemode tinyg_tidmode tinygg2 grbl marlin] 1.92   0}]}
2016/10/30 11:53:03 hub.go:122: sendjson {"P":"/dev/ttyACM0","Data":[{"Id":"startup5","D":null},{"D":"{\"sr\":n}\n","Id":"tinygInit-cmd45","Pause":0},{"D":"{\"qr\":n}\n","Id":"tinygInit-cmd46","Pause":0},{"D":"{\"hp\":n}\n","Id":"tinygInit-cmd47","Pause":0},{"D":"{\"fb\":n}\n","Id":"tinygInit-cmd48","Pause":0},{"D":"%\n","Id":"tinygInit-cmd49","Pause":0},{"Id":"startup6","D":null}]}
2016/10/30 11:53:03 serial.go:606: Sending err back:  We could not find the serial port /dev/ttyACM0 that you were trying to write to.

This is what comes out, no matter what I do. If I have both usb ports hooked up or just the native port.

I have tried using the suggested script at the bottom of the flashing wiki page, but it makes no difference. Everything executes with no errors, but I still cannot connect to the board.

I am on ubuntu 16.10 and I have compiled a custom G2 bin, but I don’t think that is the source of this problem since it worked fine for a while and I have made no changes to it since then. I am trying a prebuilt image now, but I cannot see how that would make any difference.

Should I be posting this to the community of SPJS instead? Or might the problem be with G2?