Thanks for the tip about the mkclean - unfortunately it didn't work...
HOWEVER
Deleting the .sub file did. Looking at the logs, I think it's actually trying to grab all the subs from the .sub file despite the fact that I set Subtitles to "None". In the plex logs I'm seeing what looks like a load of requests to grab various sections of the .sub file. I'm going to grab a clean log (one without media scans and whatnot) and submit it, as I don't think plex should be doing that. I don't know if it's a PMS issue or a PHT issue, though.
The lines I'm seeing are basically:
Sep 26, 2014 14:51:23 [0xa532bb70] DEBUG - Request: [192.168.0.13:48833] GET /library/streams/113905?encoding=utf-8&X-Plex-Token=xxxxxxxxxxxxxxxxxxxx (4 live)
Sep 26, 2014 14:51:23 [0xa532bb70] DEBUG - * encoding => utf-8
Sep 26, 2014 14:51:23 [0xa532bb70] DEBUG - * X-Plex-Token => xxxxxxxxxxxxxxxxxxxx
Sep 26, 2014 14:51:23 [0xa532bb70] DEBUG - We found auth token (xxxxxxxxxxxxxxxxxxxx), enabling token-based authentication.
Sep 26, 2014 14:51:23 [0xa532bb70] DEBUG - Came in with a super-token, authorization succeeded.
Sep 26, 2014 14:51:23 [0xa532bb70] DEBUG - Request range: 0 to 0
Sep 26, 2014 14:51:23 [0xb3e06b70] WARN - We didn't receive any data from 192.168.0.9:50034 in time, dropping connection.
Sep 26, 2014 14:51:23 [0xa66b3b70] DEBUG - Request: [192.168.0.13:48834] GET /library/streams/113905.sub?X-Plex-Token=xxxxxxxxxxxxxxxxxxxx (3 live)
Sep 26, 2014 14:51:23 [0xa66b3b70] DEBUG - * X-Plex-Token => xxxxxxxxxxxxxxxxxxxx
Sep 26, 2014 14:51:23 [0xa66b3b70] DEBUG - We found auth token (xxxxxxxxxxxxxxxxxxxx), enabling token-based authentication.
Sep 26, 2014 14:51:23 [0xa66b3b70] DEBUG - Came in with a super-token, authorization succeeded.
Sep 26, 2014 14:51:23 [0xa66b3b70] DEBUG - Request range: 0 to 0
Sep 26, 2014 14:51:23 [0xa66b3b70] DEBUG - Content-Length of /mnt/user/Video/Movies/Movie/Movie.sub is 71489536.
Sep 26, 2014 14:51:55 [0xa66b3b70] DEBUG - Request: [192.168.0.13:48835] GET /library/streams/113906?encoding=utf-8&X-Plex-Token=xxxxxxxxxxxxxxxxxxxx (3 live)
Sep 26, 2014 14:51:55 [0xa66b3b70] DEBUG - * encoding => utf-8
Sep 26, 2014 14:51:55 [0xa66b3b70] DEBUG - * X-Plex-Token => xxxxxxxxxxxxxxxxxxxx
Sep 26, 2014 14:51:55 [0xa66b3b70] DEBUG - We found auth token (xxxxxxxxxxxxxxxxxxxx), enabling token-based authentication.
Sep 26, 2014 14:51:55 [0xa66b3b70] DEBUG - Came in with a super-token, authorization succeeded.
Sep 26, 2014 14:51:55 [0xa66b3b70] DEBUG - Request range: 0 to 0
Sep 26, 2014 14:51:55 [0xa532bb70] DEBUG - Request: [192.168.0.13:48836] GET /library/streams/113906.sub?X-Plex-Token=xxxxxxxxxxxxxxxxxxxx (3 live)
Sep 26, 2014 14:51:55 [0xa532bb70] DEBUG - * X-Plex-Token => xxxxxxxxxxxxxxxxxxxx
Sep 26, 2014 14:51:55 [0xa532bb70] DEBUG - We found auth token (xxxxxxxxxxxxxxxxxxxx), enabling token-based authentication.
Sep 26, 2014 14:51:55 [0xa532bb70] DEBUG - Came in with a super-token, authorization succeeded.
Sep 26, 2014 14:51:55 [0xa532bb70] DEBUG - Request range: 0 to 0
Sep 26, 2014 14:51:55 [0xa532bb70] DEBUG - Content-Length of /mnt/user/Video/Movies/Movie/Movie.sub is 71489536.
Sep 26, 2014 14:52:00 [0xad575b70] DEBUG - NetworkServiceBrowser: PLAYER departed after not being seen for 181.882406 seconds: 192.168.0.8
Sep 26, 2014 14:52:23 [0xa532bb70] DEBUG - Request: [192.168.0.13:48837] GET /library/streams/113907?encoding=utf-8&X-Plex-Token=xxxxxxxxxxxxxxxxxxxx (3 live)
Sep 26, 2014 14:52:23 [0xa532bb70] DEBUG - * encoding => utf-8
Sep 26, 2014 14:52:23 [0xa532bb70] DEBUG - * X-Plex-Token => xxxxxxxxxxxxxxxxxxxx
Sep 26, 2014 14:52:23 [0xa532bb70] DEBUG - We found auth token (xxxxxxxxxxxxxxxxxxxx), enabling token-based authentication.
Sep 26, 2014 14:52:23 [0xa532bb70] DEBUG - Came in with a super-token, authorization succeeded.
Sep 26, 2014 14:52:23 [0xa532bb70] DEBUG - Request range: 0 to 0
Sep 26, 2014 14:52:23 [0xa66b3b70] DEBUG - Request: [192.168.0.13:48838] GET /library/streams/113907.sub?X-Plex-Token=xxxxxxxxxxxxxxxxxxxx (4 live)
Sep 26, 2014 14:52:23 [0xa66b3b70] DEBUG - * X-Plex-Token => xxxxxxxxxxxxxxxxxxxx
Sep 26, 2014 14:52:23 [0xa66b3b70] DEBUG - We found auth token (xxxxxxxxxxxxxxxxxxxx), enabling token-based authentication.
Sep 26, 2014 14:52:23 [0xa66b3b70] DEBUG - Came in with a super-token, authorization succeeded.
Sep 26, 2014 14:52:23 [0xa66b3b70] DEBUG - Request range: 0 to 0
Sep 26, 2014 14:52:23 [0xa66b3b70] DEBUG - Content-Length of /mnt/user/Video/Movies/Movie/Movie.sub is 71489536.
There are a lot more lines of basically the same thing, that's just a snippet. Then it finally gets to:
Sep 26, 2014 14:54:34 [0xa66b3b70] DEBUG - Client [4160dc38-a4dc-45d9-bb32-219dda1dc6b1] reporting timeline state playing, progress of 0/8154198ms for guid=com.plexapp.agents.imdb://tt1843866?lang=en, ratingKey=34285 url=, key=/library/metadata/34285, containerKey=/playQueues/342, metadataId=34285
EDIT:
Update - logs added to first post