I don't think that you can disable gapless anymore like you used to. But then nor do I think that it's anything that you should notice on a day to day basis like it used to either.
If it's going through your whole library, it sounds like maybe that info got corrupted or something and it's having to go back and reanalyze everything. Then again, gapless has been buggy for the last few releases so perhaps it's a symptom of that.
I'd just let it do its thing and see if it's just a short term issue.