Well...
I tried creating a new DVB-S test network and assigning it to one of the tuners on the 6991SE card, and then created and scanned a known good mux:
2017-08-19 12:32:06.936 mpegts: 4020V in Test - tuning on TurboSight TBS 6991SE DVBS/S2 frontend : DVB-S #0:B
2017-08-19 12:32:06.938 subscription: 001D: "scan" subscribing to mux "4020V", weight: 6, adapter: "TurboSight TBS 6991SE DVBS/S2 frontend : DVB-S #0:B", network: "Test", service: "Raw PID Subscription"
2017-08-19 12:32:08.322 tbl-base: nit: 4020V in Test: invalid checksum (len 115, errors 1)
2017-08-19 12:32:09.839 mpegts: 4020V in Test scan complete
2017-08-19 12:32:09.839 subscription: 001D: "scan" unsubscribing
2017-08-19 12:33:54.771 service-mapper: Test/4020V/CHANNEL-1: success
It actually did find all the services on the mux, but displayed that one error ("tbl-base: nit: 4020V in Test: invalid checksum (len 115, errors 1)").
I then mapped a known good service to a channel. It was only when trying to play the channel that everything fell apart:
2017-08-19 12:34:30.561 htsp: Got connection from 192.168.1.24
2017-08-19 12:34:30.566 htsp: 192.168.1.24: Welcomed client software: Kodi Media Center (HTSPv25)
2017-08-19 12:34:30.576 htsp: 192.168.1.24 [ Kodi Media Center ]: Identified as user 'hts'
2017-08-19 12:34:47.201 mpegts: 4020V in Test - tuning on TurboSight TBS 6991SE DVBS/S2 frontend : DVB-S #0:B
2017-08-19 12:34:47.202 subscription: 001E: "192.168.1.24 [ hts | Kodi Media Center ]" subscribing on channel "CHANNEL-1", weight: 150, adapter: "TurboSight TBS 6991SE DVBS/S2 frontend : DVB-S #0:B", network: "Test", mux: "4020V", provider: "Acme", service: "CHANNEL-1", profile="htsp", hostname="192.168.1.24", username="hts", client="Kodi Media Center"
2017-08-19 12:34:48.210 TS: Test/4020V/CHANNEL-1: H264 @ #1281 Continuity counter error (total 1)
2017-08-19 12:34:48.232 TS: Test/4020V/CHANNEL-1: AC3 @ #1282 Continuity counter error (total 1)
2017-08-19 12:34:48.247 TS: Test/4020V/CHANNEL-1: AC3 @ #1284 Continuity counter error (total 1)
2017-08-19 12:34:48.262 TS: Test/4020V/CHANNEL-1: AC3 @ #1283 Continuity counter error (total 1)
2017-08-19 12:34:48.781 tbl-base: sdt: 4020V in Test: invalid checksum (len 352, errors 1)
2017-08-19 12:34:50.231 tbl-base: nit: 4020V in Test: invalid checksum (len 115, errors 1)
2017-08-19 12:34:58.216 TS: Test/4020V/CHANNEL-1: H264 @ #1281 Continuity counter error (total 5235)
2017-08-19 12:34:58.239 TS: Test/4020V/CHANNEL-1: AC3 @ #1282 Continuity counter error (total 409)
2017-08-19 12:34:58.261 TS: Test/4020V/CHANNEL-1: AC3 @ #1284 Continuity counter error (total 231)
2017-08-19 12:34:58.291 TS: Test/4020V/CHANNEL-1: AC3 @ #1283 Continuity counter error (total 222)
2017-08-19 12:35:04.031 tbl-base: sdt: 4020V in Test: invalid checksum (len 352, errors 2)
2017-08-19 12:35:08.223 TS: Test/4020V/CHANNEL-1: H264 @ #1281 Continuity counter error (total 10062)
2017-08-19 12:35:08.268 TS: Test/4020V/CHANNEL-1: AC3 @ #1282 Continuity counter error (total 807)
2017-08-19 12:35:08.268 TS: Test/4020V/CHANNEL-1: AC3 @ #1283 Continuity counter error (total 434)
2017-08-19 12:35:08.268 TS: Test/4020V/CHANNEL-1: AC3 @ #1284 Continuity counter error (total 451)
2017-08-19 12:35:08.351 tbl-base: cat: 4020V in Test: invalid checksum (len 30, errors 1)
2017-08-19 12:35:08.817 tbl-base: pat: 4020V in Test: invalid checksum (len 64, errors 1)
2017-08-19 12:35:14.902 tbl-base: pmt: 4020V in Test: invalid checksum (len 90, errors 1)
2017-08-19 12:35:17.253 subscription: 001E: "192.168.1.24 [ hts | Kodi Media Center ]" unsubscribing from "CHANNEL-1", hostname="192.168.1.24", username="hts", client="Kodi Media Center"
2017-08-19 12:35:30.703 htsp: 192.168.1.24 [ hts | Kodi Media Center ]: Disconnected
Again this did NOT happen under 4.0. Tvheadend had no problems playing this channel until I upgraded to 4.2. Coincidentally, additional support for CA cards was added in 4.2. Coincidentally, every TBS card I have tried that does NOT have a CA slot works perfectly in 4.2. Is it possible that when adding support for CA cards in 4.2, the condition where a card is in use that has CA slots, but where nothing is plugged into the CA slots, wasn't tested properly? Otherwise, there are a lot of strange coincidences here, and I'm finding it difficult to believe they aren't in some way related. In any case, even if the CA slot has nothing to do with it, there's still a problem, because a card that worked great under 4.0 now doesn't work under 4.2.
@saen acro, just so I know who I am talking to, are you an actual Tvheadend developer? And if so, did you personally work on the code that added support for CA slots in 4.2?