You need to get the program to start at startup to stop the drive disapearing the good news is you know you can access the drive so it's just a case of using 'startup applications' in the system-preference menu. You remember the command you used with own email that is the same one just copy and paste from the terminal  into the command part of the add dialog of 'startup applications' but include the path to where you extracted the pogoplug exe. As you can see with mine I installed it to my home folder in it's own folder - '/home/xxxxxx/pogoplug/'

 /home/xxxxxx/pogoplug/./pogoplugfs --user xxxxxx@someemail.com --password xxxxxx --mountpoint /media/pogoplug

Then restart and it should appear on your desktop.

Ian