Funny...when we were using Great Lakes Scrip a few years ago, they REQUIRED that you be 501c3. Not sure if that's still their policy, but it was then. (we ended our program for lack of participation; the company was great). I've done a lot of digging in the 501c3 thing, and though I'm not an expert, I can't imagine how that would jeopardize your 501c3. It's jsut another form of fundraising.
I am surprised to see so many of you do scrip. Our school actually belongs to PTA but, I have inquire for years about doing a scrip program. Our Treasurer was told at our PTA meeting that we could not do scrip because we may risk losing our tax exempt (501c3) status. Have any of you heard this? Or do you know how you all get around that?