I'm confused about the inconsistent application of questions about tools and whether they're on topic or not.

For example:

http://academia.stackexchange.com/questions/10597/how-can-i-use-the-ms-onenote-application-for-my-lierature-search was closed and received downvotes.

http://academia.stackexchange.com/questions/10578/how-to-read-and-take-notes-on-research-papers is open and has a number of upvotes.

The close votes for one is that it is off-topic (rather than, for example, being "not constructive"; arguably the second question shows that the some solutions have been attempted, whereas the first one does not illustrate this preparation) but at the core these questions have similar styles.