I'm using version 2.9.8 of S-gear 2 with the latest version of Reaper (v 6.53), recording in 96k at 256 sample size. The problem occurs also with 44.1k and 128 and 512 sample sizes, so I don't think that's the issue.
This only happens with S-gear and not with my other guitar plugins, where the loop I recorded will start over without any click. As soon as I turn S-gear on and play the loop the click occurs when it loops back. It's very distracting and basically prevents me from getting into the zone with my practice.
I think it may have to do with Reaper's automatic latency compensation? I don't know a lot about that, but I do see that the other guitar plugins will show how many samples out of 256 they're "using", next to the CPU usage indicator. Waves GTR is using 81 out of 256, Neural DSP 128 out of 256, but S-gear is using 0 out of 0? Something seems odd about that.
Edit: I just checked with Guitar Rig 5 which also reads 0/0 spls and I don't get the click with that. So the cause may be something else.