I’ve faced this problem at of the client and it seems even after increasing the time out value it didn’t work.
Troubleshooting this kind of issues is mess so the solution is to use preferred DC and run Power Shell to save it.
Here is the Power shell command:
$ups = Get-SPServiceApplication -Identity GUID of the UPA
Set-SPProfileServiceApplication $upa-UseOnlyPrefferedDomainControllers 1
That solved the issue!!!! no more time outs and can see the all the OU’s.