Recently my paper was accepted for a conference and I presented the paper without any problem. At the final stages the publication committee is raising concerns my paper has significant plagiarism. However, the major source listed as plagiarized was my master's thesis from which I adapted my paper. So, does this count as a plagiarism since the paper was adapted from my thesis - is it a proper flag? Please let me know your thoughts!
No, this type of reuse is not a problem. You (with the help of your thesis advisor, most likely) should push back.
Essentially there is an exception to rules around reuse of materials between theses/dissertations and published articles or conference publications. Typically the duplication is handled via a footnote on the first page.
Yes, it very much might be self-plagiarism. Take a look at this text, specifically the guidelines and the reasoning behind calling self-plagiarism an ethical breach. Rule of the thumb: do not publish the same thing twice. Reusing lectures you're giving? Sure, go ahead. Conference talks? Better not (personally, I find it completely acceptable to do that in case of "in-house" conferences adjacent to larger ones but in that case the committee is fully aware of it and is giving the green light).