I haven't been able to figure out exactly what causes the issue but I've had the Output Folder and Package Type in Media Settings change without me doing so. When this happens the Package Type in Install Parameters gets changed from Mixed to 64-bit for X64 also. I will update this topic once I have been able to reproduce the issue consistently but until then I thought I should bring it to your attention.
So far I have only noticed that it changes when I make a change to the AIP file.