Thanks for the OS information! I am unable to replicate this in my Ubuntu browser. However, I have put in a fix that would deal with this into the next version.
For now there isn't really any content beyond the Nightmare Heart, so consider the game won! Towards the end of this week I will push the first content update that adds new cards and content beyond the Nightmare Heart.
All upgrades through skills are temporary, unless you buy it at a higher rank. The "Upgrade" keyword does state this.