EVALUATION

Using the spy++ tool to monitor activation and focus related messages on the JFrame. 
When the bug is reproduced:
===========================
clicking on the applet's "Go!" button
-------------------------------------
<00001> 0014065A S WM_PARENTNOTIFY fwEvent:WM_LBUTTONDOWN xPos:246 yPos:18
<00002> 0014065A R WM_PARENTNOTIFY
<00003> 0014065A S WM_MOUSEACTIVATE hwndTopLevel:0014065A nHittest:HTCLIENT uMsg:WM_LBUTTONDOWN
<00004> 0014065A R WM_MOUSEACTIVATE fuActivate:MA_ACTIVATE
<00005> 0014065A S WM_ACTIVATEAPP fActive:True dwThreadID:00000000
<00006> 0014065A R WM_ACTIVATEAPP
<00007> 0014065A S WM_ACTIVATE fActive:WA_CLICKACTIVE fMinimized:False hwndPrevious:(null)
<00008> 0014065A R WM_ACTIVATE

below shows after closing the new browser window
-------------------------------------------------
<00009> 0014065A S WM_ACTIVATE fActive:WA_INACTIVE fMinimized:False hwndPrevious:(null)
<00010> 0014065A R WM_ACTIVATE
<00011> 0014065A S WM_ACTIVATEAPP fActive:False dwThreadID:000014D4
<00012> 0014065A R WM_ACTIVATEAPP
<00013> 0014065A S WM_ACTIVATEAPP fActive:True dwThreadID:000014D4
<00014> 0014065A R WM_ACTIVATEAPP
<00015> 0014065A S WM_ACTIVATE fActive:WA_ACTIVE fMinimized:False hwndPrevious:(null)
<00016> 0014065A R WM_ACTIVATE
<00017> 0014065A S WM_ACTIVATE fActive:WA_INACTIVE fMinimized:False hwndPrevious:(null)
<00018> 0014065A R WM_ACTIVATE
<00019> 0014065A S WM_ACTIVATEAPP fActive:False dwThreadID:000010A8
<00020> 0014065A R WM_ACTIVATEAPP

When the bug isn't reproduced - using old plugin:
=================================
left click on the applet's "Go!" button
----------------------------------------
<00001> 00160614 S WM_PARENTNOTIFY fwEvent:WM_LBUTTONDOWN xPos:254 yPos:16
<00002> 00160614 R WM_PARENTNOTIFY
<00003> 00160614 S WM_MOUSEACTIVATE hwndTopLevel:00160614 nHittest:HTCLIENT uMsg:WM_LBUTTONDOWN
<00004> 00160614 R WM_MOUSEACTIVATE fuActivate:MA_ACTIVATE
<00005> 00160614 S WM_ACTIVATEAPP fActive:True dwThreadID:00000000
<00006> 00160614 R WM_ACTIVATEAPP
<00007> 00160614 S WM_ACTIVATE fActive:WA_CLICKACTIVE fMinimized:False hwndPrevious:(null)
<00008> 00160614 R WM_ACTIVATE

the following appears right away upon the new browser window shown
------------------------------------------------------------------
<00009> 00160614 S WM_ACTIVATE fActive:WA_INACTIVE fMinimized:False hwndPrevious:(null)
<00010> 00160614 R WM_ACTIVATE
<00011> 00160614 S WM_ACTIVATEAPP fActive:False dwThreadID:00001574
<00012> 00160614 R WM_ACTIVATEAPP

When the problem happened, the WM_INACTIVE never got delievered to the JFrame in time; it was delievered after the new browser window was closed.