Please report bugs to http://www.adobe.com/go/wishso that our QE team can take a look at them. I can't say for sure, but it sounds like the app isn't recovering from sleep mode -- the other issues are probably a symptom of that.
I fixed the bug by some sort of improvisation ,although I still believe it is something to do with AIR environment
Now ,concerning the bug. Actually the problem was as following.
First : it happens only from 1024 resolution and downwards in any Machine .but if a machine has a resolution number selection up to 1200(width) it will happen too. The reason is that my app width is 1200- bigger then screen res. Now I found that when we revoke the app after the PC exited the sleep mode ,somehow it shrinks invisible docked app window to screen resolution -1024 in our case and because this res is smaller than app width it becomes cut off. I did not find this specific problem solution in the Web but in few blogs some experts are talking about some problems with AIR and Sleep Mode . So I had to improvise . What I have done is quite simple solution but it works when you undock the App there is line of code that assigns once again the default app with (1200px) to the whole application and it is not being cut off anymore ! . But yes I am going to submit it to the AIR bugs list.
By the way. How can I submit this bug? The link you have posted denies my IP .
Thanks a lot.