I encountered this problem in VM Workstation 9.0.1 as well. Clear install CentOS v6.3, stock kernel or just compile install latest 3.4.2x kernel, then install the VMTools that came with VM WS 9.0.1. Then this problem will happen about 1/3 of reboot. I haven't enabled NTP, on AMD Phenom hosts.
Hope their will be a solution soon! Is it the reason why VM WS 9.0.2 still not released yet?
Thanks!