I am seeing similar error at my ESXi server. I tried all revisions of the diskCreate in vaainas50-cert folder. I copied each of them over to the ESXi server.
VMware workbench VAAI NAS certification 2.1.0-810318
/tmp # ./diskCreate
Error during version check: The system call API checksum does not match (0x4f3299f0 [kernel] != 0x1bf36cd5 [user]).
/tmp # vmware -v
VMware ESXi 5.0.0 build-914586
But on my workbench in /opt/vmware/VTAF/storage50-cert/VTAF/Test/Storage/StorageCert/CertTools/, I do not have 914586, I only have folders range from 469512 to 799733, which appears to be for ESXi 5.1.x.