I would think that having one probe under a hide might up the humidity a bit, but I don't know about THAT much. Is it a humid hide or just a normal hide? And are the thermometers the same brand/model?

90% humidity is definetly too high in my opinion... I'm letting my humidity get up to around 85% AT MOST and that's cause he's in shed right now.

If that's really how high the humidity is, I would try and get it down, but as long as the whole tank isn't 90%, and it's not wet, then I wouldn't worry too much.