Not all parts in model printing?  

Not all parts in model printing?

So my MK3 has worked flawlessly since last year when I got it up and running. I've been hesitant to update the firmware or Slic3r (Prusa Edition) since it's been absolutely trouble free, even with difficult prints. Last week I finally updated to the latest 3.6.0 firmware and current Slic3r (v2.2.4). Initially prints seemed fine...but today I ran into an odd problem when printing a batch of 5 small tricopter parts all at once.

These five parts are all in the same Sketchup model, exported as one STL and sliced in Slic3r (v2.2.4). The parts are definitely each manifold and slice without errors and are visible on the plate in Slic3r. I've printed multiple parts like this many times with no issue in the past. These are not large parts and don't take up that much of the plate...maybe 150x100 area.

The problem I'm having in this particular case is when the printer creates the skirt it only encapsulates the area around 2 of the 5 parts and starts printing only those parts. Once it gets part of the way into these parts, it now attempts to start printing the other parts which leads to a crash/failure.

I've tried rolling back to an earlier firmware (3.5.2) and slicing with an earlier version of Slic3r but neither helped. I haven't tried both yet (i.e. earlier slicer + earlier firmware) but it seems like neither is a factor. I have not tried rolling all the way back to my original firmware (which I think was v3.3.1). If I separate the parts and print them in two separate files (2 in one file and 3 in another) I can print them with no issue.

Scratching my head here...not sure what the issue might be...any input would be appreciated. Seems like I must be missing something obvious but I'm not sure what...