Yeah, I got exactly the same issue with the new cores.
Only PAL-hires (non-interlaced) works OK, everything else makes the Indy hang and don't output anything, the only way to recover is to power-cycle.
Also, pressing "apply" in the config-tool makes the Indy hang, forcing a new power-cycle.
When I install the latest update and do "update all" it updates cores 0-5 and 7 (not core 6?) then the Indy stops sending output to my monitor (tested multiple times with 3 different monitors).
I'm currently using the latest config-tool with the older beta cores, and it appears to work OK.