DON'T USE TIF!! Gahh! /endspaz

TIF has no standard specification, so each program can interpret the data differently. TGA is much better, as it's still capable of RGBA and compression, and is handled by each application the exact same way.

Some programs will set alpha pixels to white, some to black, some to green, etc. It all depends. What you need to do is use a compositing application, such as after effects. That will solve many of the questions stated here.

(Also, FYI; never render in JPG. It washes out the color, has low quality; and compresses the hell out of the image)