I think that problem resolved. I checked server logs (Xcode -> Service log) and find that device list and provisioning profiles are correct downloaded after relogin to team (saved to
/Library/Server/Xcode/Data/ProvisioningProfiles
(from comments)
With the release of OS X Server 3.2.1, the provisioning profiles have been relocated to
/Library/Developer/XcodeServer/ProvisioningProfiles
with _teamserver owner). Server download only automatic generated profiles ("iOS Team Provisionong Profile: bundle id") and you should choose this profile in target settings and commit to your VCS.