Hmm - as I said, we had only one bad day in two weeks which went through the beginning of October.
The second "worst" day was this here:http://www.summitpost.org/a-pyrenees-classic/758257
and we climbed a 3000er during the day. You never know but from your original post I see you are aware of that.
We always take two or three weeks of vacation in September and we always end up on the south side of the Alps main ridge. Dolomites, Julian Alps, anything around Vinschgau / Val Venosta. So far I can only remember two vacations in which we had snow, 2001 in the Dolomites and 2007 in the Julian Alps. Bad weather we had plenty, but most of the times only short spells. To me it feels like the farther you are from any kind of sea the better the weather will be. Therefore central Pyrenees or central southern Alps, anything between the Rhine River and Brenner Pass (or a bit beyond) seems safe.