An application can technically write files to anywhere in the file system that you have permission to write to, as well as off site locations such as FTP and other Online File Services. So depending on the decisions of the individuals involved with writing your particular piece of software, that preference could be anywhere in the file system that you have access too.
From a programmers perspective: Application Position and Size are two different values and do not need to be saved together, or saved at all and can be honestly hard coded into the application.
Typically programs save User related preferences to the Registry or the users folder which can be found by typing %UserProfile% (e.g. c:\users\YourName in the case of Win7/Vista/Win8) in the File Explorer address bar.
- HKEY_CURRENT_USER\Software\< application name>\
If it is a "System wide" setting that effects all users, then typically those settings are going to be possibly in the Public or All Users folder (not likely however), In the registry, or in the program files folder.
- < Publicly accessible folder where everyone can access such as All Users>
Depending on how easy the company that wrote your software wanted to make it for you to change those values, depends on how easy it will be to change those values. If they are using, for example, an encryption algorithm to save the application settings to a file or registry then good luck decrypting the file to make that change.
- If it is a built in application setting (hard Coded), your out of luck.
- If this happens on one user, but not another, then it's in the user folder or current user registry. Delete the Registry key to reset it, or the application folder to reset it. Careful this might break the system or application forcing a re-installation.
- If this happens on all users, and changed recently, then it's in a public folder or registry. Delete the applications registry keys, uninstall and remove all file locations for the application, re-install.
- If the company is willing to release where their registry keys and folder locations store information, ask them on their forums, through email, or call them. You would be surprised how willing tech support is to help.
 It might also be worth mentioning there are two ways that an app generates dialog boxes. One is using the windows dialog box, the other is to create it's own. Typically dialog boxes created by the application (created by the programmer who is having the application generate it), is a set size and hard coded.