Proper Network Activation problem has been fixed in wp 3.3.1 or not?

In short: No, it hasn’t been fixed – You should use the plugin instead.

In Detail: Activation hooks should work for the main site properly. For subsites (or as Nacin pointed out: for all sites), you should use a proper upgrade routine. Not that I double that 1).

1) Note to myself: When a core dev says that core internals are lame, then this should tell me something. Not shure what exactly, but I’ll think about it.

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