I have a similar issue with a show recorded OTA from CBS. Version 6 only shows one audio track and it is the descriptive (English) track. Version 5 shows both tracks. Increased 'MBytes to scan at file open' (1000) with no luck. Disabled 'Ignore transport stream maps' with no luck.
Version 6 info output:
File: Name : S:\My TiVo Recordings\Plex DVR\To Process\The Neighborhood.S04E06.ts
Size : 2.160 GB
Duration : 00:29:57.03
Mux type : TS Stream
Video: Encoding : MPEG2
VideoStreamID : x31
Frame rate : 29.97 fps
Encoding size : 1920 x 1080
Display dimensions : 1920 x 1080
Aspect ratio : 16:9
Header bit rate : 14.334 Mbps
VBV buffer : 1192 KBytes
Profile : Main@High
Progressive : Prog or Int
Chroma : 4:2:0
Bit rate : 9.046 Mbps
Captioning : EIA 608/708
Field order : Top field first
Audio Stream: 1 (Primary) Codec : AC3
Format : AC3 stream
Channels : 2.0
PID : x35
PES Stream Id : xBD
Bit rate : 192 Kbps
Sampling rate : 48000
Sample size : 16 bits
Version 5 info output:
File: Name : S:\My TiVo Recordings\Plex DVR\To Process\The Neighborhood.S04E06.ts
Size : 2.160 GB
Duration : 00:29:57.03
Mux type : TS Stream
TS mux rate : 9.578 Mbps
Video: Encoding : MPEG2
VideoStreamID : x31
Frame rate : 29.97 fps
Encoding size : 1920 x 1080
Display dimensions : 1920 x 1080
Aspect ratio : 16:9
Header bit rate : 14.334 Mbps
VBV buffer : 1192 KBytes
Profile : Main@High
Progressive : Prog or Int
Chroma : 4:2:0
Bit rate : 8.678 Mbps
Captioning : EIA 608/708
Field order : Top field first
Audio Stream: 1 (Primary) Codec : AC3
Format : AC3 stream
Channels : 5.1
Language : eng
PID : x34
PES Stream Id : xBD
Bit rate : 384 Kbps
Sampling rate : 48000
Sample size : 16 bits
Audio Stream: 2 Codec : AC3
Format : AC3 stream
Channels : 2.0
Language : spa
PID : x35
PES Stream Id : xBD
Bit rate : 192 Kbps
Sampling rate : 48000
Sample size : 16 bits