Yeah, I get that too sometimes. I find that if I boot into another OS like Android, then go back to Sailfish it helps, though even then, I sometimes need to reboot again before it works. But with enough reboots, I can always get it to sort itself out without resorting to anything drastic.
However, I notice that when this problem occurs, Safestrap is also incorrectly reporting the battery level at 99% - I don't know what that implies?
Also, are you using the safe slot? I am, and I don't remember this problem happening when I used a virtual slot, but that might just be because I didn't use it very long in a virtual slot.