Thank you your help, that was anyway obvious. And it didn't help.
But the problem is much deeper here guys.
I just still don't get why Apple doesn't do something with it. I don't think so that problem is for us only.
I cleared the bookmarks in my safari last night. Looked like it cleared. I intended to clear my bookmarks on the server of iCloud. I thought that happened. But it didn't!
When I switched bookmarks sync back on my iPad it was still getting a old version. But how? Where from?
So the conclusion is a, the server wasn't clear or b, the iPad use some different "method" to reach the server and it gets a old version of my bookmarks. Doesn't matter how many times I would do the reset, delete bookmarks things... the problem, the malfunktion is with iCloud. It is 100% fact for me now.
I've tested the problem on different macs and I can tell you something is very wrong with iCloud.
When I was switch on the bookmarks sync on an other mac it was downloading a same old bookmarks than iPad. After I clear all bookmarks on this "new" mac and I was waiting. On my iMac didn't clear the bookmarks at all. Because the server problem I think. After I switched off my bookmarks sync on my iMac and switched back. It asked meg the merge question (stupid, because you have no any other logical choice) and I merged it. Suddenly the other "new" mac got my bookmarks! So this parts of test was worked well. But only this.
Nothing else, as you read my discreption here... Nothing!
So what is it if not the iCloud malfunction? Apple should let the users (experinced users) to delete or handle their bookmarks like the Xmarks does! Apple should agree or learn from them or from other smart guys.
Don't get me wrong, I like Apple I really do. Steve, still is my mentor, ideal... but Steve not with us anymore unfortunately.
If anyone knows a official chanel to write Apple with this "serious" problem, please let me know as I'll write them about this case.
I just cannot belive they didn't reconized this problem yet... and they still didn't fix it!
iCloud would be the best feautre ever made by anyone... just it doesn't work. So ... we are nowhere with it!
Sorry it didn't help. How long did you wait after turning off iCloud bookmark syncing on all your devices?
I would wait at least a few hours (maybe 24) before turning back on bookmark syncing on the device you want all the others to sync to.
All I can say is I've resolved this issue for five of my friends and myself. Best of luck!
CubaCalian: I use two Mac's and two iDevices. I can not get the Mac's to sync bookmarks after a restart. Once the Mac is started, I can "force" a sync by using the iCloud system preference to cycle the Bookmark choice. I can also create a new bookmark on the Mac to "force" a sync. From then on, until the next restart, bookmarks are synced. This happens on both Mac's, each running 10.7.3. I even tried signing out of iCloud altogether on the two Mac's, restarting, then signing back in. But that didn't fix the problem either. So it seems as if a sync isn't occuring at startup, as it should. The two iDevices have been working okay. The fact that your Mac's are now syncing okay, after a reasonable period of time and restarts, leads me to believe that reliable sync is a possibility - I just can't figure out how to get it working on my Mac's. I always find this kind of thing frustrating.
With 1 Mac, 1 iphone 4S and and 1 Ipad 2, I get a sync on iphone and ipad with an "old" version of my bookmarks.
I tried the procedure above, and what I got was a delete of all my "new" bookmarks on the Mac.
There is now a problem on Safari where new bookmarks do not appear from the bar but appear in the bookmarks list in Safari.
The Iphone and the Ipad do not get the new bookmarks.
Weird, quick and dirty development
The only technical question is files time stamps.
Oh, yes, Apple have always problems with dates and times.