Sig .40 mags in a 9mm?

Yes if you have a newer 229 in 9mm but no if you have an older version. Sig changed the frame last year so that the 9mm frame is the same as the .40 frame. Previous 9mm 229's had a narrower mag well and the .40 mags were too wide to fit.
 
My experience is 9mm in a Sig 40S&W mag jam up when trying to extract .

I've had no problem doing it for a couple of mags with a (read: one) Mec-Gar extended baseplate magazine. My testing is far from thorough, but the majority of people that I've heard talk about it have had it work for them. Were you using the typical plastic/metal mags?
 
Sig switched to the new configuration for the 9mm last year so if your 229 is older than that you probably have the dedicated 9mm frame. The new versions also have the "new" long extractor and the full height rear serations on the slide.
The .40 mags work in my latest 229 with a build date of June 2011. The mags insert and lock in place but I have never tried loading them with 9mm and seeing if they would function properly. I have used 9mm 226 mags in my 229's and they fit and function perfectly although as mentioned they do stick out a bit from thr bottom of the mag well.
 
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