Is this with Stellarmate appliance (which has a built in RTC), or with Stellarmate OS (which will only have a RTC if you have installed one on the GPIO)?

With a USB GPS you are not going to get a synchronisation that is entirely accurate (expect it to be around a second out), and if chronyd/ntpd has access to better time sources then it will label the GPS time as too out of date to sync to.

As I'm not using Stellarmate, I'm probably not going to be much help, but it is strange that you say ntp / chrony are not working, firstly, you should only run one or the other, you can't run both. I think they both try to bind to a port udp/123, so if one is running already then the other won't start properly.

You should probably try and find some relevant logs (in /var/log) which would tell you why something is not starting properly.

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