We've actually seen a pretty big discrepancy in our last few meets between the lap time being sent to Lynx and the photo finish time this fall too. We're running the most recent ART version on all computers and have tried with sync source None (which is what we usually use) and Internal.
We evaluate every runner anyway so it's not a huge deal, but did have a Lynx camera drop mid race last week and had to rebuild directly from the chip reads.
Our primary usage for ART in cross country is to help speed evaluation by sending the chip read to Lynx and then hitting shift so the most recent chip read appears.