Standard computer clocks are generally terrible at maintaining an accurate time over long periods. This is because a clock on a computer is just a counter, and the counter needs to be updated at exact time intervals to be accurate; computers are incapable of doing this, however, because they only perform operations at discrete times defined by their chip clock frequency, the period of which will never be an exact multiple of the required time interval. Here is a link to a more complete description of this and related issues.
I imagine a mere 2.5k isn't a lot if you're bent on HFT - your pool is certainly higher anyway.
are there any blogs or articles written by quants in the field who have developed HFT systems?? most of this stuff is proprietary, so very hard info to find externally
I wonder how you get around this, there was mention of a GPS clock, but they can set you back a good $2500.
Has anyone else on here encountered this issue, and how did you fix it?
Never heard about this. The only blog which is close that I'm aware about it's a Matt Davey's Tales from the Trading Desk. Not HFT's quant but he covers a lot essential things in his blogs from order management and communication with exchanges through appropriate data strucutres, algorithms and tecnhologies to general trends in algo trading.