About recognizing the USB connection to the Intel Galileo:
1) One of the most frequent and periodically reported problem is due to driver installation problems.
Possible Fix/es: sometimes it is enough to follow the step-by-step guide starting at IoT - Step 1: Make a bootable micro SD card | Intel® Software. If the problem persists, another way of solving the driver issue has been reported: Issue with connecting galileo gen 2 to win 8.1 computer, , .
2) Hardware issues: defective cables, using SUB hubs, USB 3.0 instead of USB 2.0 ports. None of these results in "always a problem", but in "sometimes a problem".
About losing USB connection:
It has been very frequent using early versions (2014-2015) of yocto in the SD, not so frequent now (since 2016 versions). The reported symptom has been that: a) everything works as expected about uploading sketches, the uploading process reports errors and the sketch is not uploaded anymore. Possible Fix/es: change USB port or, rather drastically reboot the computer.
About Arduino compatibility: before starting a project involving several devices/modules, check the Intel Galileo shield compatibility report: Shield Testing Report for Intel® Galileo Board, Intel® Galileo Gen 2...