Can you make up some full parameters so you can share with us (i.e. let us see the secret key / challenge / response for a Standard and a YK4 - obviously not the one you're using)?
I just ran a couple tests and I don't see any differences. I tried with a YubiKey Standard, YubiKey 4, and YubiKey NEO:
(With Personalization Tool v 3.1.24 on Windows 10):
*Slot 2
*Require user input not selected
*Variable input
*Secret key - 6cc335d6b04852ea46178fda1d8849c65e166e68
Same credential programmed into slot 2 of all three YubiKeys. I then used ykchalresp in Command Prompt:
Code:
c:\ykpers-1.17.1-win64\bin>ykinfo -a
serial: 2245696
serial_hex: 224440
serial_modhex: ddfffc
version: 2.4.2
touch_level: 2307
programming_sequence: 3
slot1_status: 1
slot2_status: 1
vendor_id: 1050
product_id: 10
c:\ykpers-1.17.1-win64\bin>ykchalresp -2 0123456789012345678901234567890123456789012345678901234567891234
03ac3c14fb27e88a46268f3822bf226d89286016
c:\ykpers-1.17.1-win64\bin>ykinfo -a
serial: 4282000
serial_hex: 415690
serial_modhex: fbghkc
version: 3.4.7
touch_level: 10759
programming_sequence: 3
slot1_status: 1
slot2_status: 1
vendor_id: 1050
product_id: 116
c:\ykpers-1.17.1-win64\bin>ykchalresp -2 0123456789012345678901234567890123456789012345678901234567891234
03ac3c14fb27e88a46268f3822bf226d89286016
c:\ykpers-1.17.1-win64\bin>ykinfo -a
serial: 4227930
serial_hex: 40835a
serial_modhex: fcjegl
version: 4.2.7
touch_level: 519
programming_sequence: 3
slot1_status: 1
slot2_status: 1
vendor_id: 1050
product_id: 407
c:\ykpers-1.17.1-win64\bin>ykchalresp -2 0123456789012345678901234567890123456789012345678901234567891234
03ac3c14fb27e88a46268f3822bf226d89286016