Since the task of showing the presentation files is entirely up to the software viewers installed on your PC, the result will be the same with or without SlideDog.
But on a general note, presentation files may not always act and look the same on different platforms and versions of presentation software. For example, a PPTX-file made with special effects only available in PowerPoint 2013 will not look the same when viewed in PowerPoint 2007.
You should always check your presentation files in advance on the computer you intend to use for your live presentation.
Another rule-of-thumb is that you should always embed external resources when possible. For instance, if you try to show a PowerPoint with non-standard fonts without embedding them or making sure they are installed on the target computer, independent of SlideDog the text might not be shown correctly. More information on embedding fonts can be found on PPTFAQs web pages