Alright, the actual problem is that right-clicking for Layer 2 to copy isn't showing up correctly in the properties on the left. However it does actually copy.
It is probably the same code that affects how Explicit Paste works. When you copy a tile in Locations, it shows tile X0, Y0, L0 in memory, whichever tile that corresponds to. At some point in the future, I plan to change how the tile preview works, though I am not sure when that will be.
...But is v2.50 compatible with v2.00 Flux files?
Yes.
Problem 3... The drop down boxes in the Tile Properties window seem to be vertically flipped. South changes North, North changes South.
Correction: The box is correct. The map window is not. Every tile in the map window is vertically flipped.
You will need to be much more specific.
---T.Geiger