This is not just a problem between Linux and WIndows but against any 2 machines. Time naturally drifts on machines. The longer a machine goes without syncing with an internet time server the worse it gets. Windows syncs regularly provided it has INet access but I don't know about Linux.
This is a machine management issue. You should ensure your servers are syncing regularly to an inet time server. Then you should just add a fudge factor for how much drift you are OK with. For example if you are doing hourly calculations then a drift of +-10 minutes might be fine but if you are doing every 5 minutes then perhaps 1 min is good enough. Provided the servers are syncing regularly then the differences should be very small.