Mesh animations DO run automatically. Normally anyway. With statemachine controllers you can turn them on/off (PlayAnim/StopAnim commands or something like that). I can't really say much about why they wouldn't run for you automatically without more info. Perhaps, if you place them via equipnodes, or if they inherit some kind of class/behavior, they might be turned off. I don't really know, I have gone only so far with testing..., and it's been 2+ years since I looked at SH4, longer even for SH3 :]
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