Sorry, I see what you mean about the IOIOLib logs now. I'm using the most recent version, version 5, and a bluetooth connection between the Android and IOIO.
Here is the log when I first open the app. All "blar" tags are my own generated tags.
05-20 17:27:21.921: D/IOIOConnectionRegistry(23052): Successfully added bootstrap class: ioio.lib.impl.SocketIOIOConnectionBootstrap
05-20 17:27:21.921: D/IOIOConnectionRegistry(23052): Bootstrap class not found: ioio.lib.android.accessory.AccessoryConnectionBootstrap. Not adding.
05-20 17:27:21.931: D/IOIOConnectionRegistry(23052): Successfully added bootstrap class: ioio.lib.android.bluetooth.BluetoothIOIOConnectionBootstrap
05-20 17:27:21.931: D/IOIOConnectionRegistry(23052): Bootstrap class not found: ioio.lib.android.device.DeviceConnectionBootstrap. Not adding.
05-20 17:27:21.951: I/blar(23052): main activity being created
05-20 17:27:22.021: I/blar(23052): AndroidApplicationHelper create()
05-20 17:27:22.021: I/blar(23052): AndroidIOIOConnectionManager create()
05-20 17:27:22.031: I/blar(23052): main activity starting
05-20 17:27:22.031: I/blar(23052): AndroidApplicationHelper start()
05-20 17:27:22.031: I/blar(23052): AndroidIOIOConnectionManager start()
05-20 17:27:22.041: I/blar(23052): main activity resuming
05-20 17:27:22.051: D/IOIOImpl(23052): Waiting for IOIO connection
05-20 17:27:22.051: V/IOIOImpl(23052): Waiting for underlying connection
05-20 17:27:22.071: V/BluetoothIOIOConnection(23052): Attempting to connect to Bluetooth device: IOIO (5C:82)
05-20 17:27:23.131: V/BluetoothIOIOConnection(23052): Established connection to device IOIO (5C:82) address: 00:1B:DC:06:5C:82
05-20 17:27:23.131: V/IOIOImpl(23052): Waiting for handshake
05-20 17:27:23.131: V/IOIOImpl(23052): Querying for required interface ID
05-20 17:27:23.141: V/IOIOImpl(23052): Required interface ID is supported
05-20 17:27:23.141: I/IOIOImpl(23052): IOIO connection established
This is what happens when scan() is called, and reconnection of the IOIO is successful. The main activity had been destroyed and recreated.
05-20 17:27:27.671: I/blar(23052): scan() called
05-20 17:27:27.701: I/blar(23052): main activity pausing
05-20 17:27:28.531: I/blar(23052): main activity stopping
05-20 17:27:28.531: I/blar(23052): AndroidApplicationHelper stop()
05-20 17:27:28.531: D/IOIOImpl(23052): Client requested disconnect.
05-20 17:27:28.531: V/BluetoothIOIOConnection(23052): Client initiated disconnect
05-20 17:27:28.531: D/IOIOImpl(23052): Client requested disconnect.
05-20 17:27:28.531: I/IOIOProtocol(23052): IOIO disconnected
05-20 17:27:28.531: I/blar(23052): IOIO_thread disconnected
05-20 17:27:28.541: D/IOIOBaseApplicationHelper(23052): IOIOThread is exiting
05-20 17:27:28.541: I/blar(23052): AndroidIOIOConnectionManager stop()
05-20 17:27:34.171: I/blar(23052): main activity being destroyed
05-20 17:27:34.171: I/blar(23052): AndroidApplicationHelper destroy()
05-20 17:27:34.171: I/blar(23052): AndroidIOIOConnectionManager destroy()
05-20 17:27:34.191: I/blar(23052): main activity being created
05-20 17:27:34.221: I/blar(23052): AndroidApplicationHelper create()
05-20 17:27:34.221: I/blar(23052): AndroidIOIOConnectionManager create()
05-20 17:27:34.231: I/blar(23052): main activity starting
05-20 17:27:34.231: I/blar(23052): AndroidApplicationHelper start()
05-20 17:27:34.231: I/blar(23052): AndroidIOIOConnectionManager start()
05-20 17:27:34.251: D/IOIOImpl(23052): Waiting for IOIO connection
05-20 17:27:34.251: V/IOIOImpl(23052): Waiting for underlying connection
05-20 17:27:34.251: V/BluetoothIOIOConnection(23052): Attempting to connect to Bluetooth device: IOIO (5C:82)
05-20 17:27:34.271: I/blar(23052): main activity resuming
05-20 17:27:34.521: V/BluetoothIOIOConnection(23052): Established connection to device IOIO (5C:82) address: 00:1B:DC:06:5C:82
05-20 17:27:34.521: V/IOIOImpl(23052): Waiting for handshake
05-20 17:27:34.521: V/IOIOImpl(23052): Querying for required interface ID
05-20 17:27:34.531: V/IOIOImpl(23052): Required interface ID is supported
05-20 17:27:34.541: I/IOIOImpl(23052): IOIO connection established
This is what happens when the reconnection doesn't work:
05-20 17:27:47.001: I/blar(23052): scan() called
05-20 17:27:47.031: I/blar(23052): main activity pausing
05-20 17:27:48.811: I/blar(23052): main activity stopping
05-20 17:27:48.811: I/blar(23052): AndroidApplicationHelper stop()
05-20 17:27:48.811: D/IOIOImpl(23052): Client requested disconnect.
05-20 17:27:48.811: V/BluetoothIOIOConnection(23052): Client initiated disconnect
05-20 17:27:48.821: I/IOIOProtocol(23052): IOIO disconnected
05-20 17:27:48.821: I/blar(23052): IOIO_thread disconnected
05-20 17:27:48.821: D/IOIOBaseApplicationHelper(23052): IOIOThread is exiting
05-20 17:27:48.821: I/blar(23052): AndroidIOIOConnectionManager stop()
05-20 17:27:53.021: I/blar(23052): main activity restarting
05-20 17:27:53.021: I/blar(23052): main activity starting
05-20 17:27:53.021: I/blar(23052): AndroidApplicationHelper start()
05-20 17:27:53.021: I/blar(23052): AndroidIOIOConnectionManager start()
05-20 17:27:53.031: I/blar(23052): main activity resuming