Here's a pic of what happened when I tried to re-texture multiple prims with click-and-drag select:

This often happens even when selecting only one prim, but always with multiple prims.

I also have seen strange behavior with texture rotation and repeats per meter in prim settings.  They seem to be possessed by random number demons.  I've had to delete and re-create a few prims that wouldn't behave.

Yes, one bad texture can ruin the whole bunch!    Everything seems fine and then I add another texture and suddenly it migrates across the whole build.   Some textures just don't understand their parameters!  LOL.

A rotten childhood?    (lol.   sorry.  I just couldn't resist)

I would like to know the answer to this too!  Textures in linked prims don't seem to be playing nice with each other.   I had a haphazard stair made of cylinders that I attempted to which I attempted to apply an imported texture (by the way about 40 textures that I imported 2 nights ago disappeared from my inventory)  that didn't work so I applied another and another -- then all the textures that I had applied including blank started cycling through all the prims at different rates with some sticking and others not.   finally I got blank to stick to all most of them without rotating at all , but then color did the same thing.   

Really? Maybe I could have left my prims in place. I deleted everything.