Local IE pages not working properly

I will try and make this as painless as possible to the reader.

I have a script that searches text files located within a folder for a certain string. The script then outputs an html file with the results and opens it with IE. The files that contain the search criteria are on the page with a link created to open the text file in a separate window. I have a button that closes everything down and starts the script over to search for another string.
My first problem is when IE opens I get the yellow security alert bar. This is an annoyance that can be clicked away. I have eliminated the yellow bar by inserting this at the top of the page. <!-- saved from url=(0014)about:internet -->
The only problem with using this is the links to the text files will not work.
The second problem is the button to close down everything and open up the script again will not work, no matter what tinkering that I do. I have tried to change the security settings but since I am not that knowledgeable in the settings, I have not delved to deep. I do not want to mistakenly open up a security hole, because my wife uses IE, for all her web browsing. Just can not get her to switch to Firefox.
The script and page worked fine and my wife was using it for about 6 months but since some security updates it has stopped working. I am not sure what updates caused it to stop working.

I have been trying for several months now without seeing any daylight to the problem.

Thanks in advance for any suggestions or links to a solution.