Does this mean the GOP doesn't have a quorum-proof majority anymore?
No, those seats were vacant at the start of the session. Reps added 2, Dems added 1, so the numbers are now 59-38-1, so the GOP has just over 60% (and therefore quorum-proof) majority. I think there's another Special election though, but its a Safe Dem seat in Madison.
And once that's filled the republicans will have 59.59% of the seats - though they'd still be able to get to the quorum w/ the independent, if he chooses to turn out.
The independent caucuses with Democrats.