The "Possible Application Mismatch" message you are seeing happens at the point when the Wixel Configuration Utility tries to read the settings from the selected Wixel. It reads the settings automatically when you click on a Wixel, unless you uncheck the "Auto Read" box.
If you click "Open", it gives you a chance to select the right app. You would want to select the one that exactly matches what is on the Wixel.
If you click "Ignore", it will go ahead and read the settings from the Wixel, even though it is possible that the Wixel is running an app that is different from the file you have opened. When you recompile your app, the settings will often move to different locations in memory, so the Wixel configuration utility will be unable to properly read the settings from your Wixel and that is why you see "garbage" after clicking "Ignore".
If you click "Cancel", it will not read any settings from the Wixel. If you write to the Wixel after clicking "Cancel" then you will just be writing the file you opened along with its default settings. Since you recompiled the app, you probably don't have the exact version that is on the Wixel anymore, so "Cancel" is generally the correct button to click.
Please note that this message will also be displayed if the Wixel app has changed any of the bytes in its flash memory. In that case, it is OK to click "Ignore" because you know that all the settings are still at the same location, so it is valid to read them from the Wixel. The Wixel Configuration Utility cannot distinguish from an inconsistency caused by different apps being on the Wixel from an inconsistency caused by a Wixel writing to its own flash area.
What happens if you click "Show Details"? It should show you the number of bytes that are inconsistent, which should give you an idea of what caused the inconsistency.