2 medical softwares often can't open pdf, just after the adobe reader install but IExplorer succeded

Hello,
We have two softwares ( medical application) which open pdf via adobe reader XI.
Theses softwares often can't open pdf, just after the adobe reader install( using adobeArCleaner+Customisation Wizard XI).
At this point Internet Explorer is ok to open pdf with adobe reader...
We have to launch manually adobe reader once on the computer to make the two applications to manage openning pdf
Launching adobe reader seems to finish the installation...
Did the editors have to put an "option" when they open pdf ( to act like Internet Explorer...) ?
Thanks

I am very glad to have a so rapid answered!
Sorry I was not precise...
When the file should open,
for one application an error is happening,
for the other application which is a "web" application, an other window ( not "web") opens with adobe reader and the pdf document ( the expected behavior is to open adobe reader and the pdf file in the web window already opened)
I think that the file association is ok, if we double clik on a pdf, adobe reader is opening and then the file is opening  in adobe reader window...
If I open Internet Explorer and I search for a pdf on the web, It is openning in the same window web.
But something seems not finish for the medical softwares...

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