Note that 1.1.x devices will (should) be backwards compatible with 1.0.x networks: during the Join Accept a 1.1.x device will see that a 1.0.x network responded, which should make it fall back to 1.0.x as of that point. I know that’s not your use case. But given that, I’d really expect 1.0.4 to be either compatible with earlier 1.0.x releases, or support detection of the network using 1.0.2 (which is what the TTN community network uses) and then fall back to 1.0.2 or 1.0.3 as well.
But: those are just assumptions.
So TTN accepted the join, and as the device starts to send data uplinks it has handled the OTAA Join Accept. Another assumption: I’d guess that TTN fails to validate the MIC of those uplinks, and hence silently drops those. The MIC is calculated using the secret NwkSKey that the node will have calculated from the OTAA Join Accept. Assuming backwards compatibility, so assuming that a 1.0.4 device should work with a 1.0.2 network: if the device would have calculated a different NwkSKey or MIC then that would be a bug in the new firmware?
If you want to debug, you could capture some full LoRaWAN data uplink packets from the gateway’s Traffic page in TTN Console for both 1.0.3 and 1.0.4, and compare using an online decoder. The decoder will assume 1.0.2, just like the TTN community network does.
Be sure to make the decoder validate the MIC too, using the secret NwkSKey (and secret AppSKey) from TTN Console. (Note that the DevAddr, NwkSKey and AppSKey change for each successful OTAA join.) If validation indeed fails for 1.0.4 using the NwkSKey from TTN Console, but if the uplinks’ structures look otherwise similar, then maybe you could make the device print the secrets it calculated from the Join Accept?
I’ve not read the change log you provided, but in an unrelated other example some funny configuration like #define LORAWAN_NWK_KEY LORAWAN_APP_KEY was required to get the correct MIC for an OTAA join. Again, that’s just an unrelated example, but I would not rule out that the configuration for your device might have changed for the new firmware…