There are a lot of compatibility issues between power point and ipad presentations apps:
-different fonts
-shapes and images not presented in the same way
-different colors
-different position for images
-different diagrams

The best solution to avoid all of these issues is so simple, just save it as PDF in your windows PC, but you can use a pdf reader and present it as a book, this App can help:

*You can present your PDF file as a presentation.
*You can change de slide just moving your finger or pressing the buttons in the bar tool
*You can hide and unhide the bar tool just moving your finger up and down
*You can select any slide on the slide's left bar
*Using a laser?? No more needed, you can draw over the slide with different colors and then back to the original slide after
*Transfer the files is very easy by ussing Itunes>Ipad>apps>addfiles or open it from an email(check our Web link in the support site for a video)
*You can send the presentation for email to your clients