Extension Manager removing the whole Plug-ins folder along with the panel

Question

When I click "Remove" from the Extension Manager interface, the following has occurred--
In CS6 - When I used the Extension Manager to "remove" by clicking the "remove" button,  it removes not just the panel I installed but has removed the folders "Plug-ins>Panels>my panel". The whole hierarchy!
In CS5 - it has left the Plug-ins folder but removed  "Panels>my panel"
In CS4 - the Extension Manager is working correctly for installing and removing without removing any shell folders.
Question #1 - What do I do about my missing plug-ins for these applications? This is disastrous!
Question #2 - Is there a way to fix the CS5 and CS6 Extension Manager to not delete the shell folders, when you are just trying to remove a custom panel????
My system:
Windows Vista Ultimate
Service Pack 2
Processor Intel Core 2 Quad CPU Q9650 @3.00GHz
Memory (RAM) 8.00GB
System-64-bit
Hard Drives C: 1Terabyte - 301GB available
Z: 1 Terabyte - 309GB available

Answer 1

Also here is more info that might be germane--
I am using Extend Script Toolkit CS6 3.8.0.12 ExtendSript 2.12 ScriptUI 6.1.8 to edit and generate 1 .mxi file for use in CS5 & CS6 and another .mxi file for use in CS4.
I open the Adobe Extension Manager for CS5 to create the .mxp files for CS5 & CS6
I double click on the .mxp file and it automatically opens Adobe Extension Manager CS6 and installs the panel into Photoshop CS6
I manually open Adobe Extension Manager CS5 it is sluggish to open and shows a progress bar. Then I do a File>Open to install the panel into Photoshop CS5.
In the testing of various iterations of mypanel, I have removed the previous version of mypanel, so there is nothing showing as enabled or installed in the EM. So, are you kind of saying that if I hadn't emptied out the panel but had left my own panels in there as just disabled, rather than "removed" that the rest of the whole Plug-ins folder would still be there. Leaving something in there would have been like saving an empty seat for a friend at the theater?
The Versions of Adobe Extension Manager that I am using are:
CS6 version 6.0.2.40
CS5 version 5.0.334
CS4 Version 2.1.112 (which appears to be working as it should!)