I cannot remember if you need to run the analysis on the individual level to get it to trigger the intro detection again, but I just checked the first episode of Cheers on my server, and the XML is showing the intro marker (7th line from the bottom):
<MediaContainer size="1" allowSync="1" identifier="com.plexapp.plugins.library" librarySectionID="2" librarySectionTitle="TV Shows" librarySectionUUID="e1852d2e-6229-4093-8319-b398c0ba9007" mediaTagPrefix="/system/bundle/media/flags/" mediaTagVersion="1698860922">
<Video ratingKey="41182" key="/library/metadata/41182" parentRatingKey="41181" grandparentRatingKey="41180" guid="plex://episode/5d9c0c71170e24001f2b991d" parentGuid="plex://season/602e5b2c9b7e9c002d702bce" grandparentGuid="plex://show/5d9c080008fddd001f28f9ab" type="episode" title="Give Me a Ring Sometime" grandparentKey="/library/metadata/41180" parentKey="/library/metadata/41181" librarySectionTitle="TV Shows" librarySectionID="2" librarySectionKey="/library/sections/2" grandparentTitle="Cheers" parentTitle="Season 1" contentRating="TV-PG" summary="Bride-to-be Diane Chambers becomes the center of attention at a cozy bar called Cheers." index="1" parentIndex="1" audienceRating="8.5" parentYear="1982" thumb="/library/metadata/41182/thumb/1634826120" art="/library/metadata/41180/art/1688377057" parentThumb="/library/metadata/41181/thumb/1634826120" grandparentThumb="/library/metadata/41180/thumb/1688377057" grandparentArt="/library/metadata/41180/art/1688377057" grandparentTheme="/library/metadata/41180/theme/1688377057" duration="1496495" originallyAvailableAt="1982-09-30" addedAt="1558922629" updatedAt="1634826120" audienceRatingImage="themoviedb://image.rating">
<Media id="86179" duration="1496495" bitrate="14062" width="1920" height="1080" aspectRatio="1.78" audioChannels="2" audioCodec="eac3" videoCodec="h264" videoResolution="1080" container="mkv" videoFrameRate="24p" videoProfile="high">
<Part accessible="1" exists="1" id="86180" key="/library/parts/86180/1606089813/file.mkv" duration="1496495" file="/media/TV_Shows/Cheers (1982)/Season 01/Cheers - s01e01 - Give Me a Ring Sometime [1080p].mkv" size="2630438585" container="mkv" deepAnalysisVersion="6" indexes="sd" requiredBandwidths="14880,14590,14404,14366,14366,14366,14366,14366" videoProfile="high">
<Stream id="190585" streamType="1" codec="h264" index="0" bitrate="14062" language="English" languageTag="en" languageCode="eng" bitDepth="8" chromaLocation="left" chromaSubsampling="4:2:0" closedCaptions="1" codedHeight="1088" codedWidth="1920" colorPrimaries="bt709" colorRange="tv" colorSpace="bt709" colorTrc="bt709" frameRate="23.976" hasScalingMatrix="0" headerCompression="1" height="1080" level="40" profile="high" refFrames="4" requiredBandwidths="14656,14366,14180,14143,14143,14143,14143,14143" scanType="progressive" title="Cheers - s01e01 - Give Me a Ring Sometime" width="1920" displayTitle="1080p (H.264)" extendedDisplayTitle="Cheers - s01e01 - Give Me a Ring Sometime (1080p H.264)"> </Stream>
<Stream id="190587" streamType="2" selected="1" default="1" codec="eac3" index="1" channels="2" language="English" languageTag="en" languageCode="eng" audioChannelLayout="stereo" headerCompression="1" requiredBandwidths="224,224,224,224,224,224,224,224" samplingRate="48000" title="English Dolby Stereo" displayTitle="English (EAC3 Stereo)" extendedDisplayTitle="English Dolby Stereo (EAC3)"> </Stream>
<Stream id="190586" streamType="3" codec="eia_608" index="0" language="English" languageTag="en" languageCode="eng" embeddedInVideo="1" requiredBandwidths="14656,14366,14180,14143,14143,14143,14143,14143" displayTitle="English (Closed Captions)" extendedDisplayTitle="English (Closed Captions)"> </Stream>
<Stream id="190588" streamType="3" codec="srt" index="2" language="English" languageTag="en" languageCode="eng" requiredBandwidths="1,1,1,1,1,1,1,1" title="English" displayTitle="English (SRT)" extendedDisplayTitle="English (SRT)"> </Stream>
</Part>
</Media>
<Guid id="imdb://tt0539756"/>
<Guid id="tmdb://7643"/>
<Guid id="tvdb://252356"/>
<Director id="192545" filter="director=192545" tag="James Burrows" tagKey="5d7768a7ad5437001f74c37a"/>
<Writer id="37263" filter="writer=37263" tag="Les Charles"/>
<Writer id="37262" filter="writer=37262" tag="Glen Charles"/>
<Role id="437670" filter="actor=437670" tag="John P. Navin, Jr." tagKey="5d776835e6d55c002040d0d6" role="" thumb="https://metadata-static.plex.tv/b/people/b3445e98d154dd698367fd64c2730d7a.jpg"/>
<Role id="240617" filter="actor=240617" tag="Michael McGuire" tagKey="5d77682c5af944001f1f7e42" role="" thumb="https://metadata-static.plex.tv/people/5d77682c5af944001f1f7e42.jpg"/>
<Role id="384167" filter="actor=384167" tag="Ron Frazier" tagKey="5d77685454c0f0001f306973" role=""/>
<Marker id="63505" type="intro" startTimeOffset="82574" endTimeOffset="148526">
<Attributes id="63505"/>
</Marker>
<Extras size="0"> </Extras>
<Related> </Related>
</Video>
</MediaContainer>
I just spot checked an episode from seasons 2, 3 and 4 and they all had the intro marker.
Try going into the season view and then next to the number of episodes, click the button to select all the episodes for that season.

Next, at the top of the screen, click the 3 dots and then analyze and see if it detects the intro after doing that.

You can check the XML like I did by clicking the 3 vertical dots in the bottom right corner of the episode image from the season view, then click get info.

On the media info dialog, click on “View XML” in the bottom left corner.

-Shark2k