
The 12 pages of apps bugs hasn't taken long to appear on my iPhone 3G with iOS4 installed.
It happened after I dragged several Folders onto invisible pages then syncing the change. Doing this is a quick way to remove the apps from the Folders. Folders do not retain their structure if moved to an invisible page in iTunes. I placed the folders on the last invisible pages. There there 17 Folders in total before syncing. When syncing was complete I had the 12 pages.I hope iTunes gets some better management options -- and soon. A thousand items in a flat file is no fun.
...even though it is shown as an invisible page in iTunes:
Update: ...but not the third Sync. Now back to eleven pages. The difference is that if I move the Apple Voice Memos app to be an 'invisible', I get 12 pages with the Voices Memos app place back on page one on the subsequence sync. Running with 12 pages in OS 3.1.2 means that with each sync you never know which pages with be visible because each sync they change in some way. I've found it necessary to manually return my iPhone to eleven pages to avoid all the hassle.

I rearranged my apps. Currently there are only 349 installed on my iPhone. I moved Voice Memo off page 10 to the invisible page 12 in iTunes. I did this by bumping. I dragged Voice Memo to page 11 in iTunes which causes the last app icon to start a new blank (invisible) page 12. I swapped Voice Memo with the app icon on page 12. I moved a couple of other apps to page 12 in my rearranging. I then did an iTunes Sync. Note: This is not a Jailbreak iPhone.
When I came to use my iPhone, page 2 was blank with one app icon. Big poo smells, I thought. This has happened in the past with iPhone OS 3.1.2 but it usually means that the previous page 11 is now invisible. But when I looked, I realised that the previous page 11 was still there, only now as a *visible page 12* on my iPhone. When I went back to page 1, I saw the Voice Memo app. The one I had moved to invisible page 12 in iTunes before I did the Sync. All the other apps on the invisible page 12 have remained invisible. I've never had 12 pages of apps on iPhone OS 3.1.2, I did have on OS 2, so 12 pages on OS 3 is a first for me. I will see if the extra page disappears on the next Sync. Sent from my iPhoneTrue, I've deleted some from iTunes as well but this is the current number.
I find if I have more than 500 apps on the iPhone 3G it becomes sluggish and some apps are likely to crash. For example, the game Lemonade Tycoon Free not only crashed but would reboot my iPhone. When I removed a load of apps, leaving only 340 installed, Lemonade Tycoon Free work without problem.

Hurray!