All apps lost after synch

This morning I connected my 3GS to my laptop which was NOT on the net. I have I tunes set for manual synch yet it still goes on it's own. Anyways, after the synch is done, all of my apps were gone. Ones that were free and ones I paid for. Tried to put them back on phone in which case it told me they were synched successfully yet nothing on the phone. I ended up updating the os, tried to synch again, same results. Had to go and reset settings and they finally appeared, although in the info screen it showed they were there all the time. Also couldn't vet anything from I tunes until after the reset. I believe I'm still running the older version of I tunes. Anyone else had this problem?

http://support.apple.com/kb/HT2519

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