I came here to discuss the same exact thing. I wasn't aware that it may be related to the latest Uverse firmware. I also just happened to replace my Slingbox 350 with an M2 when I noticed this happening.
I can use the app's remote to enter channel 1010 or 1451 for example, but I cannot enter 1005, 1008, etc. It will tune to "105" an d"108" respectively. Any help would be great!