How do you work with master slides and layouts?

I just thought I'd throw this out to the community because it's based on feedback regarding my recent "flickering slides" post.

The upshot so far is that: 

1) It's normally best practice in PowerPoint to use multiple masters and layouts to cut development/editing time etc.  Most of us know this and it's certainly one of the best features of PowerPoint..

2) Articulate seems to "create" a flicker when linking slides that are built using different masters or layouts (currently with QA).  

Which kind of means that 1 and 2 (seemingly) come into conflict if you're building a course that has several backgrounds and loads of objects (that you might prefer to store in masters/layouts) - and you want it to look fast and fluid to the learner.

The advice so far is to use a single master with a single layout ... which means changing all the affected modules is going take some time given that they've been built using the aforementioned method.

So do any of you have any "best practice" examples or experiences of how to make the best use of masters/layouts and AP when using loads of backgrounds and objects?

Thanks