It's a bug in both the beta and the old firmware. The code that checks how full the card is uses 32-bit integers, which wrap around at 4GB. So when your card has just shy of a multiple of 4GB (e.g. 3.7 GBish) you get this warning. As soon as you have more than 4GB it will wrap around and think the card is almost empty...
Thankfully it's only this check that has the problem: the card info in settings correctly shows the capacity, and the actual filesystem code handles > 4GB just fine.
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