Arranging blocks causes others to be shuffled around into different regions

I've been having trouble with my blocks. Whenever I try moving multiple blocks into different regions (all at once), after pressing save many of the other (untouched) blocks get placed in random regions. For example, say I moved blocks A, B, and C into region X. Even though I didn't touch blocks D, E, or F, they will get moved into regions Y and Z. As far as I've noticed, this only happens when I move more than one block at a time.

There are a huge amount of blocks on my site that are both used and unused and I think the number of blocks is causing this to happen. I've searched on Google and the forums here and haven't seen any solutions to or reports of this problem. Is there any way to be able to move blocks in batches without having to play the game of 52 Pickup?