The Moku:Pro is quite complex, so compiling even a basic project can take 15 minutes just because of the complex routing in an FPGA of this type. This can easily take an hour or so to compile projects that are either deceptively simple, or are unintentionally complex. If you’re happy to share your code on here, maybe we can debug this further.
If the same code is taking 15 minutes to compile and other times it is taking over an hour, that may be a different issue. If this is the case, I’ll reach out to my IT team and we can look at the compile logs to understand what is happening here.