Same problem here. I'm in the final WHMCS configuration step, and that happens.
Comparing the source code between an account created via API (broken CSS) and an account created by the panel (perfect CSS), I realized that the css directory created via api is "/user/cwp_theme/EN/css", a directory that does not it exists, while in the creation by the panel it is "/user/cwp_theme/ORIGINAL/css".
It probably has something to do with the default account language setting.
In the hope that someone will solve this, because I don't know how to do it for now.