We released a fix in our release this morning (2018-07-24). In order to get things ordered correctly, you'll need to open your rule, make a change (you can change the order, then change it back to where it was, that counts), and save the rule.
We are working on an automated process that will fix this automatically for all affected rules, but that will probably not make it into a release until next week, so those negatively impacted can fix it manually now.
Technical details for those curious: under the hood, each action in a rule has an order. There were some scenarios where the order was not being saved correctly. Sometimes it didn't matter, and sometimes it caused your actions to appear in a different order than they were when you saved them (if you opened the rule again after save). The fix waits for a rule to have a change, then when it is saved, it will normalize the order of all rule components, giving them each a new order value based on what you've specified in your rule.
I just tested in my instance, taking a rule that had been working. I added some values to the "Set Variables" call and I'm now seeing the same issue where "Send Beacon" is happening before "Set Variables". I did not change the ordering at all.
This seems like it's an issue with Launch itself - something in the compiling and building of the rules?
If you go to the publishing tab inside Launch and open up your library, is the published version of the rule the latest version? You can actually click on the rule's name inside the library and see the actual version that's being published by that library and see if it matches what you expect to be seeing.
I'm also experiencing this issue. It is not exclusively when adding new actions but also when you edit existing actions. My clear variables seems to move automatically in front of my send beacon action causing none of set variables to pass. Even when trying to reposition the clear variable back in it's final place it pops back in the automatically positioned order. Thanks for getting this resolved.