I thought it could be a problem with power supply:
the first report refers to a 5V,600mA power supply, the second to a 5V,1A one.
In the first the system seems unable to determine the Serial
in the second sometimes it does but it seems unable to maintain...
Use self power USB hub to power 3G dongle. Yun's USB only feed 4.5V, hardware bug.
http://forum.arduino.cc/index.php?topic=209836.msg1541065#msg1541065
I verified: this 3G dongle works fine with Ubuntu, but only if plugged before boot.
If plugged in with system on there's no way to turn on
just like with Yun. Myabe this information could help to solve the problem...
Use Yun's MCU to control self power USB hub power, only turn it on once CPU is finished boot.
Post at https://forum.openwrt.org/ for help, It has more 3G users.