Sorry, haven't had a chance to get back on the forums until now.
what would really help is give me a specific effect to compare like "Fan effect at the 1:23 mark on model XYZ
The effects in the test sequences are all within the first 10 seconds. I guess you've probably already had a chance to check it out by now, though. Please let me know if you need me to provide any other files or information.
I also noticed differences in other effects that may help to track down this issue. For instance, curtain and bars. Try droping a curtain effect on the HOUSE OUTLINE that opens/closes in the center using my old layout in the old version. Then play the same sequence in my new layout in the new version and you should see differences in the center point. I noticed the same thing with bars. I'm sure there are other effects with similar issues too.
Here's some other interesting info that might also help. I tried playing around with the "circles" effect that's used on the arches in my test sequence. This is what I found when I tried this effect using both of my layouts (new/old) in both versions of Xlights in various combinations:
The effect does NOT work with my NEW layout in the NEW Xlights version (2016.20)
The effect does NOT work with my NEW layout in the OLD Xlights version (4.2.17)
The effect does NOT work with my OLD layout in the NEW Xlights version (2016.20)
The effect
DOES work with my OLD layout in the OLD Xlights version (4.2.17)
Hopefully this may help track down the issue.
We take backward compatibility with sequences very seriously.
I'm definitely glad to hear that!

Thanks again to all who are looking into this!

Hopefully if this is a bug, it'll save others from having possible issues when the bulk of users start sequencing later in the year. I'm probably just about the only Christmas nut who starts sequencing songs in March!
