For the last several years I have been experiencing those frequent 1-3 minute (undetectable by software nor by watchdogs; only detectable by physical browsing, constant usage of your sites; constant reloading of pages, constant checking of your mail for extended periods of time, or sometimes - accidentally) downtimes on all my sites including my mail (failed to connect). I usually detect those 103 min. outage accidentally or by constantly using my site(s) for a few minutes or longer at a time. I made "tracert domain.com" and the result seemed to be ok. So as I understand there is a connection during the 1-3 minute outage, but all sites and mail during that outage is inaccessible and returns unavailable error or nothing. I noticed it happens many times per day, every day, or almost every day. The uptime watchdog that watches all my sites for periods of every 15 minutes does not notice or "catch" these 1-3 minute downtimes. I'm afraid that even 1-3 minute downtime for say 24 times a day is insignificant, but it can still make a lot of damage to a business. I don't think it is an issue with the host. Any of you experience this FSD (frequent short downtime) or FBO (frequent brief outages)? If not, try spend 1 to 24 hours constantly browsing and reloading your sites and see if you "catch" some "couple minute downtime" or sometims it can be as little as 10-30 seconds downtime. It shouldn't remain a mystery. Let's find out what those FSD are.
It's a possibility that there has been an error on your server and the server has been configured to automatically 'restart' or 'reboot' each time such errors occur. Aside from that it could be the server making backups I suppose, but to occur that often each day I doubt that very much indeed.
If it happens at the same time every day it could be something like a scheduled job that uses so many resources that the server is unable to respond to requests during that time. A watchdog might not notice this if the server is not actually refusing connections, it's just too busy to send data on them. It would be unusual for something to use so many resources your sites are not accessible at all, but if you can't find any other explanation you should definitely check if anything is scheduled. It depends on the type of server too, for example processing on some VPSes might be halted for a few minutes while a backup is made.