Thanks! That made me keep digging. And I think I have it solved.
Here is what I found.... The incompatible item is the
"PDF Professional Filter"It gets set when one chooses to index "File Properties and Contents".
That filter prevents capturing TAGS etc where they can be used by PDF-ShellTools.
I was fooled into thinking it was the Flash player because when I loaded a new Flash Player, indexing stopped working ! ! !
It turns out that installing FLASH went in and changed my setting back to "File Properties and Contents". That of course, reset the Filter.
I did not reset the filter. I assume it was done by the FLASH installer, but you seem not to have had that problem.
Now I have FLASH running OK with IE9
PDF-ShellTools DOES pick up the TAGs and allows me to search on them.
Ugh!