I'm using PS CS3 here and I have had this problem from time to time over the years, but this time I'd like to deal with it.
I'm creating many layers and many "path layers" in a document. They all need to be contained it the same file, so I don't want to have 5 different files with 10 layers each for example. Now on to the problem:
The amount of path layers that I have exceeds the vertical distance on my monitor. So there is no negative space inside the paths palette to click and thus have no path layers selected. The result is if I go to the layers palette and delete something in that layer, whatever is in the paths layer will also be deleted. So as a temporary work around, I've been creating a blank path layer, then when that deletes there is no problem. Does this make sense.....it does in my head as I type this, but that doesn't always count:)