This issue could be caused by code generation timeout.
By default, Peripherals Tool has 15 seconds allocated for code generation (which should be more than enough). If code generation scripts do not finish their execution in 15 seconds, the code will not be generated.
The timeout can occur if the machine on which S32CT is running is slow/heavily loaded/code generation scripts are not optimized.
As a workaround for this issue, code generation timeout can be increased by adding the following argument into the s32ds.ini file (default path could be C:\NXP\S32DS.3.4\eclipse\s32ds.ini, it depends on the version of S32DS).
-Dcom.nxp.swtools.codegenscript.timeout = 60000 -> It will increase code generation timeout to 1 minute.
Or you can increase the timeout based on your environment.
Try this workaround and let me know the result.