This has just started happening to me randomly with Studio One 4.6.1. This is maddening, and it doesn't look like anyone has bothered to address this. If I expand the bit of initial audio that I recorded before the loop, all the takes are there - laterally recorded on one track, totally out of place and useless.
It doesn't look like Studio 5 has fixed this. This is a total deal breaker. Looks like it's time to kick Studio One to the curb and get a different software package.