Please try turn off the Graphics Processor and see if that helps.
Go to Lightroom Preferences from the Edit menu
Click on Performance tab
Uncheck the Graphics Processor
It's always behaved a bit flaky for me more or less like you describe with quite lazy updating of the links. This is only a problem I think when the catalog is really large. I've often had to go into Develop and back to make lightroom realize that yes, there is an actual file there! Also, it's better to update links by going to your top-level folder and relinking this to it's new location instead of doing individual files especially if you simply moved over a folder structure to your new machine. Lastly, if you are using an external disk, make sure it is not NTFS or FAT32 formatted. This can cause some issues with synchronization I have noticed so better to only use hfs+ (native filesystem for Macs). Most external disks that you buy need to be reformatted to get this which of course erases data on the disk.
That said, another thing you are describing sounds a bit like you are at v6.2 which is a really bad idea. Especially so on a Mac as this version is riddled with major slowdown bugs that can make Lightroom only barely usable both on Macs and PCs but specially so on Macs. If you are still on 6.2 you should update to 6.3 asap.
This does not seem to help, although having restarted Lightroom, it does now show all the photos correctly from one folder I was trying, but I'm not sure whether this is the result of restarting or turning off the Graphics Processor. But it doesn't help with new attempts to Locate Missing Photos unfortunately.
Flaky is just the term! I have a catalog of 102,000 photos so quite large, and am running 6.0 so it's not a 6.2 issue. My drives are formatted with MacOS Extended (journaled) which is not hfs+ as you suggest. When you say better to go to the top level folder - I'm not sure where to do this if the new folder location is not yet known to Lightroom?
That is the right disk format actually. Mac OS Extended is just what Apple calls hfs+ in the OS. What I mean with top-level folder is to find
in your hierarchy the most top-level folder that is common to both your old machine and the new machine in the browser on the left and make sure to update it's location. This will relink all the files below and usually takes fewer steps (only one if you have a single top-level folder) when your moving between machines.
Thanks. But I find if I link the top-level it finds 86,000 photos, of which I'm not sure how many it would import, some of which it might duplicate. Which really makes a mess (been there!). I'll maybe try at a lower level, a bit at a time. Good idea in theory though.