Flaps animation in F16 working at Half and Full. No animation on F18 Half flaps.
#CUP_00-Stabs4All is your problem. - #CUP_00-Stabs4All - Should NOT be used with moden jets like the F/A18 because it will break the flight model and your flaps will not work properly either. #CUP_00-Stabs4All is for use with aircraft that do not have a fully modelled Autopilot.
Unload #CUP_00-Stabs4All - DO NOT add any other mods to #JTW - and you will be fine. Trying to find workarounds to get #CUP_00-Stabs4All working on the F/A18 is not the best idea. Instead, why not just learn how to fly S3's brilliant aircraft?
Here is the Manual:
https://www.mediafire.com/view/nfperf80os341p0/USMC_F-18CD_AV-8B_Manual.pdfThank you for withdrawing the comment about the F-16 animation and admitting that you broke it and then made a hasty post. This is not a good start to a working relationship - because it marks you as a poor communicator.
Let's put that to one side - I am a very patient man - and its nearly Christmas. F16 OK now, lets take a look at the F/A18E flaps animation:

Runway takeoff test - Flaps to FULL - Note rear flap position and front droops.

Takeoff configuration - Flaps to HALF - Note rear flaps up and front droops extended.

Takeoff complete - Flaps and front droops fully retracted. - Switch flaps to AUTO as you go fence out...
#CUP_00-Stabs4All - Should NOT be used with moden jets like the F/A18 because it will break the flight model and your flaps will not work properly. This is why its included as a JSGME Option - Broad flight model classfile changes should be applied in appropriate circumstances and not simply put into your mod folder automatically.
HELL YA #1 to get it !
No you weren't - I was! 
Spoil Sport!...............
Hello Hoss!
Good to see you there mate!