system time instability

[Konstantin Belousov]

On Mon, Dec 12, 2016 at 11:04:08PM +0400, Hrant Dadivanyan wrote:
> Now, when you ask, I start to suspect PPS delivery to uart again - cable
> and amplifier, but can't understand how the 100ppm error fits into that.

If you disable PPS sync in ntp config, does the machine keep time adequately ?

There might be relatively long pauses when system management mode handlers
do something in response to hw events.  E.g. if you have USB emulation of
AT keyboard enabled in BIOS, try to disable that.  And update the BIOS.