No it is not you, we are noticing that they appear to be backwards at times.
We are looking into this.
Thanks for reporting it, and sorry for the delayed reply.
The Alphas are for blending the maps in the terrain routine. GIMP does not show them correctly and they indeed have an image in them in photoshop.
We do not use mipmaps yet.
Intel(R) Core(TM)2 Quad CPU Q6600 @ 2.40GHz, 2400 Mhz, 4 Core(s), 4 Logical Processor(s), 8gb RAM, Nvidia gtx660, Windows 7 Pro 64bit