It happens only with copying from slot with lower index to slot with higher index. For example, if you copy 8th slot to 6th slot, the FX will appear at 6th slot, but if you copy FX from 3rd slot to 6th slot, it will appear at 7th slot. Reaper 6.49, but also happened in 6.47.
reaper.TrackFX_CopyToTrack(tr, 3-1, tr, 6-1, false)
reaper.TrackFX_CopyToTrack(tr, 8-1, tr, 6-1, false)
Fixed in v6.50.