Wow, ok. I don't think I've seen one so far off. Can you check the VCC line and check it really is 3.3v? The early Picos didn't have a very powerful diode and is was easy to slightly frazzle it if they got shorted - in that case it might not be getting the full voltage needed for 3.3v, which might be affecting the RTC speed?
But yes, if you need deep sleep I think using an external low speed oscillator (or a whole external RTC like http://www.espruino.com/DS3231) is probably the only solution.
Newer Espruino Originals actually have an RTC crystal on them so that could be a good choice?
I think the NucleoF401RE doesn't use the RTC so it wouldn't actually keep time properly with deep sleep at all.
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