Another news worth mentioning is this update doesn't require you to reboot iOS whenever installing or upgrading this app in the future. So forget the old and tiring process of rebooting iOS and smile now!
Saurik also mentioned that Substrate is compatible with a semi-tethered jailbreak idea. Oh one more thing, Redsn0w was also updated today, it is Redsn0w 0.9.10b3 now with the purpose to fix the MobileSubstrate issue. Therefore looks like everything is okey now.
To download MobileSubstrate 0.9.3955, open Cydia and hed to Changes tab, continue with refreshing your sources. You will see it is there, if that's so then install MobileSubstrate 0.9.3995 to your devices.
Hope it works for you!