This guide does not apply to Android/Kindle users as there is no Game Center on these devices. Game Center is owned by Apple.
Please note that this system is separate to Apple's iCloud system, as it caters for all platforms (iOS and Android).
Do NOT rely on automatic saves when visiting the party boat or neighbours, it is unreliable!
Manual cloud save often!
The problem:
Game Center friends don't see changes to your town while you're logged into both Game Center AND Facebook. (Or the other way 'round, which is rare).
This is an acknowledged bug: "Some players have experienced having different save data available for each account, which should not be the case. The team is currently correcting this problem."
The cause:
While my earlier explanations of "two clouds" was the best way to describe it, technically it's all the same cloud at Firemonkeys' (Firemint's) cloudsever. You just access it with two different logins (one being your Game Center ID, the other your Facebook ID).
Theoretically these accounts are linked, in practise this works only partially. When logged in on both accounts, you will see the most recent cloud save for the linked accounts, but your facebook account is seen as the main account for cross-device portability. This leaves the Game Center ID lagging behind.
Side note: Those who are digging around the internet might have noticed that cloudcell is owned by ndWare PTY ltd. This is the very same company. (See also: ndWare company info and history).
The solution (or work-around):
1. Cloud save manually

2. Log off from your Game Center and in the game log off from Facebook.
3. Double-Press the home button on your device (the square), the list of active apps should show in the bottom panel. Long-press one of the apps, you'll see red icons with a minus in it appearing on all apps. Close them all. (Minimum are SFP and GC)
4. Hold the power button of your device, then swipe to turn off.
5. Wait at least 5 mins, longer might be necessary especially the first time. (This is to allow your accounts to be un-linked on the server).
6. Power on, start Game Center and log in, next start the Sims FP.
7. Go into the cloud icon and verify the time since the last saved game, if it is longer ago than your last save (at step 1) you are looking at the Game Center linked account. If not, you'll have to wait (at least with cloud saving). It can take over 24 hours to unlink.
Reversing:
8. If the above went fine, log out from Game Center, force close the apps (minimum are SFP and GC) and turn off your device, wait a few minutes, then turn it on.
9. Start the Sims Freeplay, then login on Facebook through the key-hole icon. If Game Center pops up, do not log in, but tap Cancel!
10. Go into the cloud icon and check when your last cloud save was, this should be the one from step 1, not step 7. Repeat from step 8 if necessary.
11. Cloud save when/if needed.
12. Before using Game Center again, you'll have to repeat the above steps to disconnect your Facebook account (this includes turning off your device and waiting!), then log in on Game Center.
I hope this helps in cloud saving for both accounts, I've had varying success with this, sometimes it took me only 10 minutes, but also over 12 hours to be able to save (to GC) or even over 24 hours to unlink the two when accidentally being logged in on both again.
I have reported this as a bug at FM's support site, but no replies to it yet.