Applications have all changed place?

Now i know that this might sound like not much however, i synced my iphone at 8 am this morning and on my iTunes it said that it was removing my applications and then adding them back in. However after it did this all my applications are now scattered everywhere and not in the places where i had put them.
As i said i know that this might sound silly but i have a lot of applications and i spent a LOT of time putting my business apps together, games together etc and now they are all over the place.
Is there a way of getting it back to the way it was before?
Any help is appreciated! Thank you!

no they were not unchecked from iTunes. All it said on Itunes as it was syncing was 'removing apps' and then it said installing apps and they were all installed again?

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