In my limited experience such an issue can be due to "whatever", especially considering and comparing the very different experiences by Blogospherianman vs. the OP. Audio Snap operations (and similar) are actually quite complicated ones going deep in the material, so they can possibly (?) conflict with, say, any VST or VSTi which is able to mangle with the project material in a similar way, even if the VST isn't loaded in the project in question (but has a complicated install structure, not only single .dll).
I wouldn't be surprised if even different hardware combinations could give such results.
Well...just pondering..
OOPS: I just noticed it's a bundle file you're trying to Audio Snap. That could be the key!You can not, for example, save groove clips in bundle file.