A rather long post, which I hope will put to rest some fears...
In my recent past as a professional programmer, I wrote several installer scripts of the type being discussed here. What the "Find Glyph" installer is doing is entirely normal practice; in fact, it is more polite than many in warning you that it is going to install "system" files. Most major software packages (virtually everything from Microsoft, for example) install numerous "system" files without your knowledge. These are normally "Dynamic Link Library" (DLL) files, which are standard libraries of routines used by several programs. If a DLL file required by the program you are installing is not already on your computer, the installer script will put it there for you, since the program won't run without it. The presence or absence of the DLL file is not necessarily related to what version of Windows you have; you could have the most recent version and still be missing DLL files required by some programs.
DLL files are not always "operating system" files (most, in fact, are not), and installing one that is not yet on your computer is not "modifying the operating system." A new DLL file will not harm your system. However, problems can arise when a badly-written installer script replaces a DLL that already exists on your system (there are rules about when an installer script is allowed to do this, but sloppy programmers ignore rules). In this case you could end up with an older version of the file, or a version not intended for your configuration; if this happens, the new program may run just fine, but all the other programs that depended on the replaced DLL file may no longer work. (This problem is known to Windows programmers as "DLL Hell".)
You should never install a program obtained from a source you do not trust. If you trust the source, or others you trust verify the integrity of the program, you can install it without worry. You should, of course, scan every downloaded file for viruses.
I have examined the files that "Find Glyph" installs; they are all standard Microsoft files required by programs created with Microsoft Visual Basic. If they are not already on your system, it is only because you have not previously installed this type of program. In my opinion, it is safe to install Find Glyph.
I would be willing to examine other "suspect" programs and report to the list. Perhaps we could create a set of links to "verified" programs that are of use to digital medievalists.
David
David Badke