I was having this same problem where the amount of posts on the categories of my JAM based theme did not correspond to the WP setting. Also when I tried a custom query to limit the amount of posts per page the resulting pagination links failed, 404.

I did not attempt the function method as outlined on your link since it sounds like it does not always, ever?, work.

To fix this issue, I activated the Carrington Blog theme, went to it's theme options page and set the desired about of posts per page, then activated my custom JAM based theme; the setting held over and the right amount of items displays on my theme now. I'm using the latest core, so it should work for you as well.

This error really drove me completely nuts for a week, I did not realize what was causing the problem and tried a hundred ways to get around it before I realized it was being caused by the framework itself. In future releases of JAM it'd be nice to have this issue resolved some how out of the box