So, doing a bit of exploring and I've hit some fun.
Was walking past Swiftperch with my character so stopped in and grabbed the Teleport point and the Chocobokeep, then walked on to Aleport and did the same... except now I can't go from Aleport to Swiftperch by Chocobo.
'Tis a minor issue, but all the same, quite irritating.
Don't know if that's the only one that doesn't work but I'm sure time will tell.