kernel warning in logs: set_rtc_mmss can't update from 0 to 58

VMWare does have some suggestions in there knowledge base on how to configure the ntp client in your guest os. First thing is to make sure the vmware-toolbox timesync is disabled, as you only want ntp to update the time.

From Timekeeping best practices for Linux guests:

This is their sample /etc/ntp.conf:

tinker panic 0
restrict 127.0.0.1
restrict default kod nomodify notrap
server 0.vmware.pool.ntp.org
server 1.vmware.pool.ntp.org
server 2.vmware.pool.ntp.org
driftfile /var/lib/ntp/drift 

The first line (tinker panic 0) allows for big time jumps. (e.g. the system state was saved/restored)

An alternative would be to disable ntp in your guest and enable the vmware-tools time syncing.

Are you running the latest kernel version for CentOS 6.4? I'd try booting with clocksource=acpi_pm. Also, I'd do ntpdate -u tick.usno.navy.mil && hwclock --systohc and let things sit. If things continue, then add divizor=10 as well.

Honestly, I suspect the problem is partly to do with the code in your particular kernel for setting and reading the real time clock - that's what gets you the error message. The other part is due to virtual time interrupts not being delivered regularily enough or the timer interrupt handler not scaling the kernel time correctly - and this is what gets you the clock drift.

Forcing ntp to be more aggressive is just a crutch for the problem, unfortunately.

Is there a newer kernel available to you? That might be your safest bet. Good Luck.