On my journal anyway, S1 comment times are in GMT. S2 comment times are in GMT +7. Had my journal in both during the past few days, and figured it out.
However, the FAQ says:
The timestamps on comment pages shown in a LiveJournal site scheme display in the timezone of the LiveJournal servers, which is US Pacific Standard Time (-800 GMT) or, when applicable, US Pacific Daylight Time (-700 GMT). The timestamps on comment pages shown in the journal's own style display in the GMT timezone.
I really don't think this is accurate. I'm not sure what its deal is, but I know i'm not the only one who's had issues. Maybe this is the wrong place for it and this is a bug.
Edit: Potential change to italicized part:
The timestamps on LiveJournal comment pages display in a timezone that is based on the server on which the individual journal is located. This will vary with the individual server.