The iPhone team had previously rolled out a version of Redsn0w, Redsn0w 0.9.10b3, for Mac and Windows that would fix issues with MobileSubstrate-based apps after jailbreaking. The Dev team has made an entry about the version in their blog.

According to the blog, this version of Redsn0w “fixes a problem where re-running redsn0w over an existing jailbreak would cause MobileSubstrate-based apps to stop running until MS was installed again.” The team also said that the user can now re-run the redsn0w jailbreak step without worrying about it. However, it is important for the user to remember to de-select the “Install Cydia” option if it’s already installed.

If you are still having repository errors when reloading, keep in mind that this isn't a jailbreak problem or a Cydia problem, the host servers are simply being overloaded by the volume of people who are jailbreaking and installing things from the repositories,” the team further wrote. “This means that you won't find a jailbreak fix for it and that even tethered jailbreak users are having the problem because they work off of the same repositories as you are.”

Nonetheless, if auto-detection fails and redsn0w cannot find any identifying data, the user can always pre-select the appropriate 5.0.1 IPSW using Extras – Select IPSW.

(Information from Dev-team Blog)

Here are the download links for Redsn0w 0.9.10b3:

For Mac

For Windows

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