I've had this issue with the last two setups I've done:
.- OS: El Capitan.
.- FMS: 14.0.4 (with and without the "b" patch).
.- FMP: 14 (latest update).
If I perform a script that contains a "Import Records..." step it returns an error of type 100 (File not Found) and doesn't import anything. If I run the very same script in the same file but opened directly (without FileMaker Server) it works as expected.
I disabled error capture to see what happens and I get an error saying something like "File 09286742982909999999.fck could not be written in the temporary folder".
I think it has to do with System Integrity Protection because in my Yosemite server this doesn't happen, however, I find strange not to see more posts like mine.
Is there anyone else with this problem?, any suggestion?.