Sorry, I’ve only just seen this as I didn’t get any notifications. There are several reasons why your layout is not working using Sections FIx.
Firstly, SectionsFix works when it is placed inside a SectionsPro stack to (a) fix content to the bottom and (b) ensure that the other content does not collide with or overlap the bottom fixed content - this is the unique aspect of the stack. On your page, it is just placed within the Filter Item stack which will not work as designed. This is causing both vertical and horizontal alignment issues.
The problem comes when you try to mix other external stacks with a library such as Isotope. We have no control or way of knowing when the size calculation has completed. If something inside a filter item needs to calculate its size and position then there it would need to happen after the isotope calculations have completed. Exactly the same problem would happen with Match Height (which you would need in addition to SectionsPro in order to make all the item contents the same height).