Tested on 1.6.x -> 1.9.0-beta. Linux Mint 18.3 x86_64.
Upon starting IDE, Port is greyed out for up to 10minutes, after which Port is not grayed and all ACMs/ttyUSB connections are shown.

NB: I have no issues uploading scripts manually from commandline OR using eclipse-arduino plugin at anytime including during the time Arduino-IDE has port grayed.

If after Port is no longer greyed, ie: I can select port and get board-id or upload scripts, If I close the IDE, and restart it, Port is now grayed out for up to 5-10mins.