Will look at these issues.
Were you using mirror mode?
As far as the clan wars portal goes, its roughly the same speed because the fountain will block you from doing anything for a few ticks
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Edit:
Looking at the withdraw logic for cosmic runes, it will attempt to withdraw 3x the amount of unpowered orbs in your inventory. If this isn't working, then its more than likely an issue with mirror mode specifically.
Can confirm the stamina bug though, will fix it