When I run the precheck on the mpw-7a version of "caravel_user_project_analog" I get:

2022-07-29 08:01:19 - [INFO] - {{STEP UPDATE}} Executing Check 5 of 5: Consistency
2022-07-29 08:01:20 - [INFO] - HIERARCHY CHECK PASSED: Module user_analog_project_wrapper is instantiated in caravan. 
2022-07-29 08:01:20 - [INFO] - COMPLEXITY CHECK PASSED: Netlist caravan contains at least 8 instances (68 instances). 
2022-07-29 08:01:20 - [INFO] - MODELING CHECK PASSED: Netlist caravan is structural.
2022-07-29 08:01:20 - [WARNING] - SUBMODULE HOOKS CHECK FAILED: The user power port vccd1 is not connected to the correct power domain in the top level netlist. It is connected to mprj/vccd1 but it should be connected to vccd1_core.
2022-07-29 08:01:20 - [WARNING] - {{NETLIST CONSISTENCY CHECK FAILED}} caravan netlist failed 1 consistency check(s): ['SUBMODULE HOOKS'].
2022-07-29 08:01:20 - [INFO] - PORTS CHECK PASSED: Netlist user_analog_project_wrapper ports match the golden wrapper ports
2022-07-29 08:01:20 - [INFO] - COMPLEXITY CHECK PASSED: Netlist user_analog_project_wrapper contains at least 1 instances (11 instances). 
2022-07-29 08:01:20 - [INFO] - MODELING CHECK PASSED: Netlist user_analog_project_wrapper is structural.
2022-07-29 08:01:20 - [INFO] - LAYOUT CHECK PASSED: The GDS layout for user_analog_project_wrapper matches the provided structural netlist.
2022-07-29 08:01:20 - [INFO] - {{NETLIST CONSISTENCY CHECK PASSED}} user_analog_project_wrapper netlist passed all consistency checks.
2022-07-29 08:01:20 - [WARNING] - {{CONSISTENCY CHECK FAILED}} The user netlist and the top netlist are not valid.

This happens even (as shown) with the original files in the repository. So seems to me like this is an issue unrelated to my own files. Can anyone else confirm this issue?

See this thread https://open-source-silicon.slack.com/archives/C01E06TUSC9/p1657837847618959

Thanks for the reference. I was not aware of the shuttle-precheck channel.