If you create a Summoner, add an Eidolon and save both to the default characters folder, close and re-open, PCGen reports error "Unable to find master" when loading the Eidolon - whether I load the Eidolon directly for from the link on the master's Companions tab.
Windows 7 64, Java 6, Pathfinder mode, PCGen 5.17.18 only (5.17.17, 5.17.16 OK)
From the Master:
FOLLOWER:X'ran|TYPE:Eidolon|RACE:EIDOLON (BIPED)|HITDICE:0|FILE:\GameP\PCGen\PCGen51718\characters\Sheila - summoner's Eidolon - X'ran.pcg
From the follower:
MASTER:Zariel|TYPE:Eidolon|HITDICE:0|FILE:\GameP\PCGen\PCGen51718\Sheila - Aasimar summoner - Zariel.pcg|ADJUSTMENT:0
Looks like the path is not being saved correctly for the follower. The actual entry saved should have been relative in both cases to allow the pair to be saved elsewhere.
File name of master/follower is now set correctly on save.
Note that any already saved characters will have to be manually opened with their linked characters and then saved again to get the correct values.